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Unverified Commit be646878 authored by Evan Pretti's avatar Evan Pretti Committed by GitHub
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Merge pull request #4989 from epretti/fix-charmm-water-models 

Update CHARMM36 2024 and add water models
parents 6817921b 7abba925
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docs-source/usersguide/application/02_running_sims.rst
View file @ be646878
...@@ -590,31 +590,31 @@ for full references). ...@@ -590,31 +590,31 @@ for full references).
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
================================= ============================================ ===================================== =========================================
File Parameters File Parameters
================================= ============================================ ===================================== =========================================
:file:`charmm36_2024.xml` Protein, DNA, RNA, lipids, carbohydrates, and small molecules :file:`charmm36_2024.xml` Protein, DNA, RNA, lipids, carbohydrates, and small molecules
:file:`charmm36/water.xml` Default CHARMM water model (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions :file:`charmm36_2024/water.xml` Default CHARMM water model (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions
:file:`charmm36/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions :file:`charmm36_2024/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:file:`charmm36/tip3p-pme-b.xml` TIP3P-PME-B water model\ :cite:`Price2004` and ions :file:`charmm36_2024/tip3p-pme-b.xml` TIP3P-PME-B water model\ :cite:`Price2004` and ions
:file:`charmm36/tip3p-pme-f.xml` TIP3P-PME-F water model\ :cite:`Price2004` and ions :file:`charmm36_2024/tip3p-pme-f.xml` TIP3P-PME-F water model\ :cite:`Price2004` and ions
:file:`charmm36/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions :file:`charmm36_2024/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`charmm36/tip4p2005.xml` TIP4P-2005 water model\ :cite:`Abascal2005` and ions :file:`charmm36_2024/tip4p2005.xml` TIP4P-2005 water model\ :cite:`Abascal2005` and ions
:file:`charmm36/tip5p.xml` TIP5P water model\ :cite:`Mahoney2000` and ions :file:`charmm36_2024/tip5p.xml` TIP5P water model\ :cite:`Mahoney2000` and ions
:file:`charmm36/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions :file:`charmm36_2024/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions
================================= ============================================ ===================================== =========================================
The file :file:`charmm36_2024.xml` bundles everything but the water and ions into a single The file :file:`charmm36_2024.xml` bundles everything but the water and ions into a single
file. In most cases, you can simply include that file, plus one of the water models, file. In most cases, you can simply include that file, plus one of the water models,
such as :file:`charmm36/water.xml`, which specifies the default CHARMM water model such as :file:`charmm36_2024/water.xml`, which specifies the default CHARMM water model
(a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions: (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions:
:: ::
forcefield = ForceField('charmm36_2024.xml', 'charmm36/water.xml') forcefield = ForceField('charmm36_2024.xml', 'charmm36_2024/water.xml')
.. tip:: The solvent model XML files included under the :file:`charmm36/` directory .. tip:: The solvent model XML files included under the :file:`charmm36_2024/` directory
include both water *and* ions compatible with that water model, so if you include both water *and* ions compatible with that water model, so if you
mistakenly specify :file:`tip3p.xml` instead of :file:`charmm36/water.xml`, mistakenly specify :file:`tip3p.xml` instead of :file:`charmm36_2024/water.xml`,
you run the risk of having :class:`ForceField` raise an exception due to you run the risk of having :class:`ForceField` raise an exception due to
missing parameters for ions in your system. missing parameters for ions in your system.
...@@ -641,6 +641,13 @@ such as :file:`charmm36/water.xml`, which specifies the default CHARMM water mod ...@@ -641,6 +641,13 @@ such as :file:`charmm36/water.xml`, which specifies the default CHARMM water mod
`CHARMM-GUI <http://charmm-gui.org/>`_, it's easiest to load `CHARMM-GUI <http://charmm-gui.org/>`_, it's easiest to load
the PSF file directly, as discussed in Section :numref:`using-charmm-files`. the PSF file directly, as discussed in Section :numref:`using-charmm-files`.
.. warning:: Solvent model files in the :file:`charmm36_2024/` directory are
designed for use with :file:`charmm36_2024.xml`, and those in the
:file:`charmm36/` directory are designed for use with an older
release of the CHARMM force field found in :file:`charmm36.xml` and
described below. Be sure to load the correct version of the
solvent model you wish to use along with the main force field file.
.. warning:: Some residues and patches are not included in this port of .. warning:: Some residues and patches are not included in this port of
CHARMM36, either due to a lack of support for certain CHARMM CHARMM36, either due to a lack of support for certain CHARMM
features in `ParmEd <https://github.com/parmed/parmed>`_, or features in `ParmEd <https://github.com/parmed/parmed>`_, or
...@@ -764,6 +771,7 @@ File Force Field ...@@ -764,6 +771,7 @@ File Force Field
:code:`amber03.xml` Amber03\ :cite:`Duan2003` :code:`amber03.xml` Amber03\ :cite:`Duan2003`
:code:`amber10.xml` Amber10 (documented in the AmberTools_ manual as `ff10`) :code:`amber10.xml` Amber10 (documented in the AmberTools_ manual as `ff10`)
:code:`charmm36.xml` July 2017 release of the CHARMM36 force field without CHARMM36m protein parameters :code:`charmm36.xml` July 2017 release of the CHARMM36 force field without CHARMM36m protein parameters
:code:`charmm36/*.xml` Parameters for water models and ions specifically for use with :code:`charmm36.xml`
:code:`charmm_polar_2013.xml` 2013 version of the CHARMM polarizable force field\ :cite:`Lopes2013` :code:`charmm_polar_2013.xml` 2013 version of the CHARMM polarizable force field\ :cite:`Lopes2013`
:code:`charmm_polar_2019.xml` 2019 version of the CHARMM polarizable force field\ :cite:`Lopes2013` :code:`charmm_polar_2019.xml` 2019 version of the CHARMM polarizable force field\ :cite:`Lopes2013`
============================= ================================================================================== ============================= ==================================================================================
......
wrappers/python/openmm/app/data/charmm36.xml
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...@@ -103763,4 +103763,12 @@ ...@@ -103763,4 +103763,12 @@
<NBFixPair epsilon="0.8631592000000001" sigma="0.25134925534893393" type1="MG" type2="SO"/> <NBFixPair epsilon="0.8631592000000001" sigma="0.25134925534893393" type1="MG" type2="SO"/>
<NBFixPair epsilon="0.8414024" sigma="0.25219560913116723" type1="MG" type2="SS1"/> <NBFixPair epsilon="0.8414024" sigma="0.25219560913116723" type1="MG" type2="SS1"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/spce.xml
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...@@ -121,4 +121,12 @@ ...@@ -121,4 +121,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/tip3p-pme-b.xml
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...@@ -121,4 +121,12 @@ ...@@ -121,4 +121,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/tip3p-pme-f.xml
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...@@ -121,4 +121,12 @@ ...@@ -121,4 +121,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/tip4p2005.xml
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...@@ -127,4 +127,12 @@ ...@@ -127,4 +127,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/tip4pew.xml
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...@@ -127,4 +127,12 @@ ...@@ -127,4 +127,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/tip5p.xml
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...@@ -129,4 +129,12 @@ ...@@ -129,4 +129,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/tip5pew.xml
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...@@ -129,4 +129,12 @@ ...@@ -129,4 +129,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36/water.xml
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...@@ -127,4 +127,12 @@ ...@@ -127,4 +127,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.2877602859593296" type1="OG2D2" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.2877602859593296" type1="OG2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28152399493234725" type1="OG2P1" type2="SOD"/> <NBFixPair epsilon="0.31388368000000005" sigma="0.28152399493234725" type1="OG2P1" type2="SOD"/>
</LennardJonesForce> </LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField> </ForceField>
wrappers/python/openmm/app/data/charmm36_2024.xml
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wrappers/python/openmm/app/data/charmm36_2024/spce.xml 0 → 100644
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<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_spc_e.str" md5hash="5a43bf944d3d6bd537b50538ceb83560" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_spc_e.str</Source>
<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="H.J.C. Berendsen, J. R. Grigera, and T. P. Straatsma. The Missing Term in Effective Pair Potentials. J. Phys. Chem 91:6269-6271, 1987." forcefield="spc-e">H.J.C. Berendsen, J. R. Grigera, and T. P. Straatsma. The Missing Term in Effective Pair Potentials. J. Phys. Chem 91:6269-6271, 1987.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="SPCE-OH2" />
<Type class="HT" element="H" mass="1.008" name="SPCE-H1" />
<Type class="HT" element="H" mass="1.008" name="SPCE-H2" />
<Type class="OX" element="O" mass="15.9994" name="OH-O1" />
<Type class="HX" element="H" mass="1.008" name="OH-H1" />
<Type class="LIT" element="Li" mass="6.941" name="LIT-LIT" />
<Type class="SOD" element="Na" mass="22.98977" name="SOD-SOD" />
<Type class="MG" element="Mg" mass="24.305" name="MG-MG" />
<Type class="POT" element="K" mass="39.0983" name="POT-POT" />
<Type class="CAL" element="Ca" mass="40.08" name="CAL-CAL" />
<Type class="RUB" element="Rb" mass="85.4678" name="RUB-RUB" />
<Type class="CES" element="Cs" mass="132.90545" name="CES-CES" />
<Type class="BAR" element="Ba" mass="137.327" name="BAR-BAR" />
<Type class="ZN" element="Zn" mass="65.37" name="ZN2-ZN" />
<Type class="CAD" element="Cd" mass="112.411" name="CD2-CD" />
<Type class="CLA" element="Cl" mass="35.45" name="CLA-CLA" />
<Type class="CU1P" element="Cu" mass="63.546" name="CU1P-CU1P" />
<Type class="AG1P" element="Ag" mass="107.87" name="AG1P-AG1P" />
<Type class="AU1P" element="Au" mass="196.97" name="AU1P-AU1P" />
<Type class="TI1P" element="Ti" mass="47.867" name="TI1P-TI1P" />
<Type class="BE2P" element="Be" mass="9.0122" name="BE2P-BE2P" />
<Type class="SR2P" element="Sr" mass="87.62" name="SR2P-SR2P" />
<Type class="RA2P" element="Ra" mass="226.03" name="RA2P-RA2P" />
<Type class="V2P" element="V" mass="50.942" name="V2P-V2P" />
<Type class="CR2P" element="Cr" mass="51.996" name="CR2P-CR2P" />
<Type class="MN2P" element="Mn" mass="54.938" name="MN2P-MN2P" />
<Type class="FE2P" element="Fe" mass="55.854" name="FE2P-FE2P" />
<Type class="CO2P" element="Co" mass="58.933" name="CO2P-CO2P" />
<Type class="NI2P" element="Ni" mass="58.693" name="NI2P-NI2P" />
<Type class="CU2P" element="Cu" mass="63.546" name="CU2P-CU2P" />
<Type class="PD2P" element="Pd" mass="106.42" name="PD2P-PD2P" />
<Type class="AG2P" element="Ag" mass="107.87" name="AG2P-AG2P" />
<Type class="SN2P" element="Sn" mass="118.71" name="SN2P-SN2P" />
<Type class="PT2P" element="Pt" mass="195.08" name="PT2P-PT2P" />
<Type class="HG2P" element="Hg" mass="200.59" name="HG2P-HG2P" />
<Type class="PB2P" element="Pb" mass="207.2" name="PB2P-PB2P" />
<Type class="SM2P" element="Sm" mass="150.36" name="SM2P-SM2P" />
<Type class="EU2P" element="Eu" mass="151.96" name="EU2P-EU2P" />
<Type class="YB2P" element="Yb" mass="173.05" name="YB2P-YB2P" />
<Type class="AL3P" element="Al" mass="26.982" name="AL3P-AL3P" />
<Type class="SC3P" element="Sc" mass="44.956" name="SC3P-SC3P" />
<Type class="Y3P" element="Y" mass="88.906" name="Y3P-Y3P" />
<Type class="LA3P" element="La" mass="138.91" name="LA3P-LA3P" />
<Type class="CE3P" element="Ce" mass="140.12" name="CE3P-CE3P" />
<Type class="PR3P" element="Pr" mass="140.91" name="PR3P-PR3P" />
<Type class="ND3P" element="Nd" mass="144.24" name="ND3P-ND3P" />
<Type class="PM3P" element="Pm" mass="144.91" name="PM3P-PM3P" />
<Type class="SM3P" element="Sm" mass="150.36" name="SM3P-SM3P" />
<Type class="EU3P" element="Eu" mass="151.96" name="EU3P-EU3P" />
<Type class="GD3P" element="Gd" mass="157.25" name="GD3P-GD3P" />
<Type class="TB3P" element="Tb" mass="158.93" name="TB3P-TB3P" />
<Type class="DY3P" element="Dy" mass="162.5" name="DY3P-DY3P" />
<Type class="HO3P" element="Ho" mass="164.93" name="HO3P-HO3P" />
<Type class="ER3P" element="Er" mass="167.28" name="ER3P-ER3P" />
<Type class="YB3P" element="Yb" mass="173.05" name="YB3P-YB3P" />
<Type class="LU3P" element="Lu" mass="174.97" name="LU3P-LU3P" />
<Type class="U3P" element="U" mass="238.03" name="U3P-U3P" />
<Type class="PU3P" element="Pu" mass="244.06" name="PU3P-PU3P" />
<Type class="TI3P" element="Ti" mass="47.867" name="TI3P-TI3P" />
<Type class="V3P" element="V" mass="50.942" name="V3P-V3P" />
<Type class="CR3P" element="Cr" mass="51.996" name="CR3P-CR3P" />
<Type class="MN3P" element="Mn" mass="54.938" name="MN3P-MN3P" />
<Type class="FE3P" element="Fe" mass="55.854" name="FE3P-FE3P" />
<Type class="CO3P" element="Co" mass="58.933" name="CO3P-CO3P" />
<Type class="GA3P" element="Ga" mass="69.723" name="GA3P-GA3P" />
<Type class="RH3P" element="Rh" mass="102.91" name="RH3P-RH3P" />
<Type class="IN3P" element="In" mass="114.82" name="IN3P-IN3P" />
<Type class="AU3P" element="Au" mass="196.97" name="AU3P-AU3P" />
<Type class="TL3P" element="Tl" mass="204.38" name="TL3P-TL3P" />
<Type class="BI3P" element="Bi" mass="208.98" name="BI3P-BI3P" />
</AtomTypes>
<Residues>
<Residue name="SPCE">
<Atom charge="-0.8476" name="OH2" type="SPCE-OH2" />
<Atom charge="0.4238" name="H1" type="SPCE-H1" />
<Atom charge="0.4238" name="H2" type="SPCE-H2" />
<Bond atomName1="OH2" atomName2="H1" />
<Bond atomName1="OH2" atomName2="H2" />
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OH-O1" />
<Atom charge="0.32" name="H1" type="OH-H1" />
<Bond atomName1="O1" atomName2="H1" />
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT-LIT" />
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD-SOD" />
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG-MG" />
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT-POT" />
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL-CAL" />
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB-RUB" />
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES-CES" />
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR-BAR" />
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN2-ZN" />
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CD2-CD" />
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA-CLA" />
</Residue>
<Residue name="CU1P">
<Atom charge="1.0" name="CU1P" type="CU1P-CU1P" />
</Residue>
<Residue name="AG1P">
<Atom charge="1.0" name="AG1P" type="AG1P-AG1P" />
</Residue>
<Residue name="AU1P">
<Atom charge="1.0" name="AU1P" type="AU1P-AU1P" />
</Residue>
<Residue name="TI1P">
<Atom charge="1.0" name="TI1P" type="TI1P-TI1P" />
</Residue>
<Residue name="BE2P">
<Atom charge="2.0" name="BE2P" type="BE2P-BE2P" />
</Residue>
<Residue name="SR2P">
<Atom charge="2.0" name="SR2P" type="SR2P-SR2P" />
</Residue>
<Residue name="RA2P">
<Atom charge="2.0" name="RA2P" type="RA2P-RA2P" />
</Residue>
<Residue name="V2P">
<Atom charge="2.0" name="V2P" type="V2P-V2P" />
</Residue>
<Residue name="CR2P">
<Atom charge="2.0" name="CR2P" type="CR2P-CR2P" />
</Residue>
<Residue name="MN2P">
<Atom charge="2.0" name="MN2P" type="MN2P-MN2P" />
</Residue>
<Residue name="FE2P">
<Atom charge="2.0" name="FE2P" type="FE2P-FE2P" />
</Residue>
<Residue name="CO2P">
<Atom charge="2.0" name="CO2P" type="CO2P-CO2P" />
</Residue>
<Residue name="NI2P">
<Atom charge="2.0" name="NI2P" type="NI2P-NI2P" />
</Residue>
<Residue name="CU2P">
<Atom charge="2.0" name="CU2P" type="CU2P-CU2P" />
</Residue>
<Residue name="PD2P">
<Atom charge="2.0" name="PD2P" type="PD2P-PD2P" />
</Residue>
<Residue name="AG2P">
<Atom charge="2.0" name="AG2P" type="AG2P-AG2P" />
</Residue>
<Residue name="SN2P">
<Atom charge="2.0" name="SN2P" type="SN2P-SN2P" />
</Residue>
<Residue name="PT2P">
<Atom charge="2.0" name="PT2P" type="PT2P-PT2P" />
</Residue>
<Residue name="HG2P">
<Atom charge="2.0" name="HG2P" type="HG2P-HG2P" />
</Residue>
<Residue name="PB2P">
<Atom charge="2.0" name="PB2P" type="PB2P-PB2P" />
</Residue>
<Residue name="SM2P">
<Atom charge="2.0" name="SM2P" type="SM2P-SM2P" />
</Residue>
<Residue name="EU2P">
<Atom charge="2.0" name="EU2P" type="EU2P-EU2P" />
</Residue>
<Residue name="YB2P">
<Atom charge="2.0" name="YB2P" type="YB2P-YB2P" />
</Residue>
<Residue name="AL3P">
<Atom charge="3.0" name="AL3P" type="AL3P-AL3P" />
</Residue>
<Residue name="SC3P">
<Atom charge="3.0" name="SC3P" type="SC3P-SC3P" />
</Residue>
<Residue name="Y3P">
<Atom charge="3.0" name="Y3P" type="Y3P-Y3P" />
</Residue>
<Residue name="LA3P">
<Atom charge="3.0" name="LA3P" type="LA3P-LA3P" />
</Residue>
<Residue name="CE3P">
<Atom charge="3.0" name="CE3P" type="CE3P-CE3P" />
</Residue>
<Residue name="PR3P">
<Atom charge="3.0" name="PR3P" type="PR3P-PR3P" />
</Residue>
<Residue name="ND3P">
<Atom charge="3.0" name="ND3P" type="ND3P-ND3P" />
</Residue>
<Residue name="PM3P">
<Atom charge="3.0" name="PM3P" type="PM3P-PM3P" />
</Residue>
<Residue name="SM3P">
<Atom charge="3.0" name="SM3P" type="SM3P-SM3P" />
</Residue>
<Residue name="EU3P">
<Atom charge="3.0" name="EU3P" type="EU3P-EU3P" />
</Residue>
<Residue name="GD3P">
<Atom charge="3.0" name="GD3P" type="GD3P-GD3P" />
</Residue>
<Residue name="TB3P">
<Atom charge="3.0" name="TB3P" type="TB3P-TB3P" />
</Residue>
<Residue name="DY3P">
<Atom charge="3.0" name="DY3P" type="DY3P-DY3P" />
</Residue>
<Residue name="HO3P">
<Atom charge="3.0" name="HO3P" type="HO3P-HO3P" />
</Residue>
<Residue name="ER3P">
<Atom charge="3.0" name="ER3P" type="ER3P-ER3P" />
</Residue>
<Residue name="YB3P">
<Atom charge="3.0" name="YB3P" type="YB3P-YB3P" />
</Residue>
<Residue name="LU3P">
<Atom charge="3.0" name="LU3P" type="LU3P-LU3P" />
</Residue>
<Residue name="U3P">
<Atom charge="3.0" name="U3P" type="U3P-U3P" />
</Residue>
<Residue name="PU3P">
<Atom charge="3.0" name="PU3P" type="PU3P-PU3P" />
</Residue>
<Residue name="TI3P">
<Atom charge="3.0" name="TI3P" type="TI3P-TI3P" />
</Residue>
<Residue name="V3P">
<Atom charge="3.0" name="V3P" type="V3P-V3P" />
</Residue>
<Residue name="CR3P">
<Atom charge="3.0" name="CR3P" type="CR3P-CR3P" />
</Residue>
<Residue name="MN3P">
<Atom charge="3.0" name="MN3P" type="MN3P-MN3P" />
</Residue>
<Residue name="FE3P">
<Atom charge="3.0" name="FE3P" type="FE3P-FE3P" />
</Residue>
<Residue name="CO3P">
<Atom charge="3.0" name="CO3P" type="CO3P-CO3P" />
</Residue>
<Residue name="GA3P">
<Atom charge="3.0" name="GA3P" type="GA3P-GA3P" />
</Residue>
<Residue name="RH3P">
<Atom charge="3.0" name="RH3P" type="RH3P-RH3P" />
</Residue>
<Residue name="IN3P">
<Atom charge="3.0" name="IN3P" type="IN3P-IN3P" />
</Residue>
<Residue name="AU3P">
<Atom charge="3.0" name="AU3P" type="AU3P-AU3P" />
</Residue>
<Residue name="TL3P">
<Atom charge="3.0" name="TL3P" type="TL3P-TL3P" />
</Residue>
<Residue name="BI3P">
<Atom charge="3.0" name="BI3P" type="BI3P-BI3P" />
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="HT" class2="HT" k="0.0" length="0.1633" />
<Bond class1="HT" class2="OT" k="376559.99999999994" length="0.1" />
<Bond class1="OX" class2="HX" k="456055.99999999994" length="0.097" />
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.9106119321581925" class1="HT" class2="OT" class3="HT" k="460.24" />
</HarmonicAngleForce>
<AmoebaUreyBradleyForce />
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge" />
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.0" sigma="1.0" />
<Atom class="OT" epsilon="0.0" sigma="1.0" />
<Atom class="OX" epsilon="0.0" sigma="1.0" />
<Atom class="LIT" epsilon="0.0" sigma="1.0" />
<Atom class="SOD" epsilon="0.0" sigma="1.0" />
<Atom class="MG" epsilon="0.0" sigma="1.0" />
<Atom class="POT" epsilon="0.0" sigma="1.0" />
<Atom class="CAL" epsilon="0.0" sigma="1.0" />
<Atom class="RUB" epsilon="0.0" sigma="1.0" />
<Atom class="CES" epsilon="0.0" sigma="1.0" />
<Atom class="BAR" epsilon="0.0" sigma="1.0" />
<Atom class="ZN" epsilon="0.0" sigma="1.0" />
<Atom class="CAD" epsilon="0.0" sigma="1.0" />
<Atom class="CLA" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.0" sigma="1.0" />
<Atom class="AG1P" epsilon="0.0" sigma="1.0" />
<Atom class="AU1P" epsilon="0.0" sigma="1.0" />
<Atom class="TI1P" epsilon="0.0" sigma="1.0" />
<Atom class="BE2P" epsilon="0.0" sigma="1.0" />
<Atom class="SR2P" epsilon="0.0" sigma="1.0" />
<Atom class="RA2P" epsilon="0.0" sigma="1.0" />
<Atom class="V2P" epsilon="0.0" sigma="1.0" />
<Atom class="CR2P" epsilon="0.0" sigma="1.0" />
<Atom class="MN2P" epsilon="0.0" sigma="1.0" />
<Atom class="FE2P" epsilon="0.0" sigma="1.0" />
<Atom class="CO2P" epsilon="0.0" sigma="1.0" />
<Atom class="NI2P" epsilon="0.0" sigma="1.0" />
<Atom class="CU2P" epsilon="0.0" sigma="1.0" />
<Atom class="PD2P" epsilon="0.0" sigma="1.0" />
<Atom class="AG2P" epsilon="0.0" sigma="1.0" />
<Atom class="SN2P" epsilon="0.0" sigma="1.0" />
<Atom class="PT2P" epsilon="0.0" sigma="1.0" />
<Atom class="HG2P" epsilon="0.0" sigma="1.0" />
<Atom class="PB2P" epsilon="0.0" sigma="1.0" />
<Atom class="SM2P" epsilon="0.0" sigma="1.0" />
<Atom class="EU2P" epsilon="0.0" sigma="1.0" />
<Atom class="YB2P" epsilon="0.0" sigma="1.0" />
<Atom class="AL3P" epsilon="0.0" sigma="1.0" />
<Atom class="SC3P" epsilon="0.0" sigma="1.0" />
<Atom class="Y3P" epsilon="0.0" sigma="1.0" />
<Atom class="LA3P" epsilon="0.0" sigma="1.0" />
<Atom class="CE3P" epsilon="0.0" sigma="1.0" />
<Atom class="PR3P" epsilon="0.0" sigma="1.0" />
<Atom class="ND3P" epsilon="0.0" sigma="1.0" />
<Atom class="PM3P" epsilon="0.0" sigma="1.0" />
<Atom class="SM3P" epsilon="0.0" sigma="1.0" />
<Atom class="EU3P" epsilon="0.0" sigma="1.0" />
<Atom class="GD3P" epsilon="0.0" sigma="1.0" />
<Atom class="TB3P" epsilon="0.0" sigma="1.0" />
<Atom class="DY3P" epsilon="0.0" sigma="1.0" />
<Atom class="HO3P" epsilon="0.0" sigma="1.0" />
<Atom class="ER3P" epsilon="0.0" sigma="1.0" />
<Atom class="TM3P" epsilon="0.0" sigma="1.0" />
<Atom class="YB3P" epsilon="0.0" sigma="1.0" />
<Atom class="LU3P" epsilon="0.0" sigma="1.0" />
<Atom class="U3P" epsilon="0.0" sigma="1.0" />
<Atom class="PU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TI3P" epsilon="0.0" sigma="1.0" />
<Atom class="V3P" epsilon="0.0" sigma="1.0" />
<Atom class="CR3P" epsilon="0.0" sigma="1.0" />
<Atom class="MN3P" epsilon="0.0" sigma="1.0" />
<Atom class="FE3P" epsilon="0.0" sigma="1.0" />
<Atom class="CO3P" epsilon="0.0" sigma="1.0" />
<Atom class="GA3P" epsilon="0.0" sigma="1.0" />
<Atom class="RH3P" epsilon="0.0" sigma="1.0" />
<Atom class="IN3P" epsilon="0.0" sigma="1.0" />
<Atom class="AU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TL3P" epsilon="0.0" sigma="1.0" />
<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom class="HT" epsilon="4.184e-06" sigma="1.7817974362806786e-05" />
<Atom class="HX" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="OT" epsilon="0.64973336" sigma="0.3165541325296254" />
<Atom class="OX" epsilon="0.50208" sigma="0.30290556416771536" />
<Atom class="LIT" epsilon="0.00974872" sigma="0.23118821735741807" />
<Atom class="SOD" epsilon="0.1962296" sigma="0.2513670733232967" />
<Atom class="MG" epsilon="0.06276" sigma="0.2111429961992604" />
<Atom class="POT" epsilon="0.364008" sigma="0.3142645228240047" />
<Atom class="CAL" epsilon="0.50208" sigma="0.24357170953956878" />
<Atom class="RUB" epsilon="0.6276" sigma="0.3385415128933289" />
<Atom class="CES" epsilon="0.79496" sigma="0.37417746161894255" />
<Atom class="BAR" epsilon="0.6276" sigma="0.33675971545704825" />
<Atom class="ZN" epsilon="1.046" sigma="0.194215920554594" />
<Atom class="CAD" epsilon="0.50208" sigma="0.2417899121032881" />
<Atom class="CLA" epsilon="0.6276" sigma="0.4044680180357141" />
<Atom class="CU1P" epsilon="0.7748768" sigma="0.1535909390073945" />
<Atom class="AG1P" epsilon="1.2008079999999999" sigma="0.2163636626875628" />
<Atom class="AU1P" epsilon="1.4907592" sigma="0.11250269012676205" />
<Atom class="TI1P" epsilon="1.7016328" sigma="0.34401163102271065" />
<Atom class="BE2P" epsilon="0.4250944" sigma="0.007127189745122714" />
<Atom class="SR2P" epsilon="0.9572992" sigma="0.3306837861993312" />
<Atom class="RA2P" epsilon="1.2631496" sigma="0.37237784620829906" />
<Atom class="V2P" epsilon="0.6732056" sigma="0.1966569830422985" />
<Atom class="CR2P" epsilon="0.6974728" sigma="0.18872798445084948" />
<Atom class="MN2P" epsilon="0.7050040000000001" sigma="0.2144749574051053" />
<Atom class="FE2P" epsilon="0.667348" sigma="0.1924519410926761" />
<Atom class="CO2P" epsilon="0.6439176000000001" sigma="0.16527953018939576" />
<Atom class="NI2P" epsilon="0.5999856" sigma="0.13903365395298137" />
<Atom class="CU2P" epsilon="0.629692" sigma="0.129198132104712" />
<Atom class="PD2P" epsilon="0.7288528" sigma="0.16519044031758173" />
<Atom class="AG2P" epsilon="0.7752952" sigma="0.1869105510658432" />
<Atom class="SN2P" epsilon="0.7861736" sigma="0.29542201493533654" />
<Atom class="PT2P" epsilon="0.6824104" sigma="0.1420270736459329" />
<Atom class="HG2P" epsilon="0.8593936" sigma="0.2105728210196506" />
<Atom class="PB2P" epsilon="1.0016496000000001" sigma="0.3132399892981433" />
<Atom class="SM2P" epsilon="1.0242432" sigma="0.330790694045508" />
<Atom class="EU2P" epsilon="0.9907712000000001" sigma="0.3279220001730961" />
<Atom class="YB2P" epsilon="0.8593936" sigma="0.28669120749756116" />
<Atom class="AL3P" epsilon="0.44601440000000003" sigma="0.039377723341803" />
<Atom class="SC3P" epsilon="0.5899439999999999" sigma="0.19544536078562763" />
<Atom class="Y3P" epsilon="0.6928704" sigma="0.25183924964391113" />
<Atom class="LA3P" epsilon="0.7932864" sigma="0.3158592315294759" />
<Atom class="CE3P" epsilon="0.7702744000000001" sigma="0.30495463121943817" />
<Atom class="PR3P" epsilon="0.7627432" sigma="0.2956180126533274" />
<Atom class="ND3P" epsilon="0.7497728" sigma="0.2886333667031071" />
<Atom class="PM3P" epsilon="0.74266" sigma="0.29527947114043407" />
<Atom class="SM3P" epsilon="0.7351288" sigma="0.2791542043420939" />
<Atom class="EU3P" epsilon="0.728016" sigma="0.2713677495455473" />
<Atom class="GD3P" epsilon="0.7209032000000001" sigma="0.2681605141602421" />
<Atom class="TB3P" epsilon="0.7083512000000001" sigma="0.2628151218514001" />
<Atom class="DY3P" epsilon="0.6999832" sigma="0.2573628216963812" />
<Atom class="HO3P" epsilon="0.6928704" sigma="0.247794569463554" />
<Atom class="ER3P" epsilon="0.6845024" sigma="0.24362516346265717" />
<Atom class="TM3P" epsilon="0.6778080000000001" sigma="0.24029320225681233" />
<Atom class="YB3P" epsilon="0.6711136" sigma="0.23077840394707347" />
<Atom class="LU3P" epsilon="0.6644192" sigma="0.2407564695902453" />
<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.35093300000000005" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.477963424" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024/tip3p-pme-b.xml 0 → 100644
View file @ be646878
<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
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<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-b">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
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<Atom class="SOD" epsilon="0.1962296" sigma="0.2513670733232967" />
<Atom class="MG" epsilon="0.06276" sigma="0.2111429961992604" />
<Atom class="POT" epsilon="0.364008" sigma="0.3142645228240047" />
<Atom class="CAL" epsilon="0.50208" sigma="0.24357170953956878" />
<Atom class="RUB" epsilon="0.6276" sigma="0.3385415128933289" />
<Atom class="CES" epsilon="0.79496" sigma="0.37417746161894255" />
<Atom class="BAR" epsilon="0.6276" sigma="0.33675971545704825" />
<Atom class="ZN" epsilon="1.046" sigma="0.194215920554594" />
<Atom class="CAD" epsilon="0.50208" sigma="0.2417899121032881" />
<Atom class="CLA" epsilon="0.6276" sigma="0.4044680180357141" />
<Atom class="CU1P" epsilon="0.7748768" sigma="0.1535909390073945" />
<Atom class="AG1P" epsilon="1.2008079999999999" sigma="0.2163636626875628" />
<Atom class="AU1P" epsilon="1.4907592" sigma="0.11250269012676205" />
<Atom class="TI1P" epsilon="1.7016328" sigma="0.34401163102271065" />
<Atom class="BE2P" epsilon="0.4250944" sigma="0.007127189745122714" />
<Atom class="SR2P" epsilon="0.9572992" sigma="0.3306837861993312" />
<Atom class="RA2P" epsilon="1.2631496" sigma="0.37237784620829906" />
<Atom class="V2P" epsilon="0.6732056" sigma="0.1966569830422985" />
<Atom class="CR2P" epsilon="0.6974728" sigma="0.18872798445084948" />
<Atom class="MN2P" epsilon="0.7050040000000001" sigma="0.2144749574051053" />
<Atom class="FE2P" epsilon="0.667348" sigma="0.1924519410926761" />
<Atom class="CO2P" epsilon="0.6439176000000001" sigma="0.16527953018939576" />
<Atom class="NI2P" epsilon="0.5999856" sigma="0.13903365395298137" />
<Atom class="CU2P" epsilon="0.629692" sigma="0.129198132104712" />
<Atom class="PD2P" epsilon="0.7288528" sigma="0.16519044031758173" />
<Atom class="AG2P" epsilon="0.7752952" sigma="0.1869105510658432" />
<Atom class="SN2P" epsilon="0.7861736" sigma="0.29542201493533654" />
<Atom class="PT2P" epsilon="0.6824104" sigma="0.1420270736459329" />
<Atom class="HG2P" epsilon="0.8593936" sigma="0.2105728210196506" />
<Atom class="PB2P" epsilon="1.0016496000000001" sigma="0.3132399892981433" />
<Atom class="SM2P" epsilon="1.0242432" sigma="0.330790694045508" />
<Atom class="EU2P" epsilon="0.9907712000000001" sigma="0.3279220001730961" />
<Atom class="YB2P" epsilon="0.8593936" sigma="0.28669120749756116" />
<Atom class="AL3P" epsilon="0.44601440000000003" sigma="0.039377723341803" />
<Atom class="SC3P" epsilon="0.5899439999999999" sigma="0.19544536078562763" />
<Atom class="Y3P" epsilon="0.6928704" sigma="0.25183924964391113" />
<Atom class="LA3P" epsilon="0.7932864" sigma="0.3158592315294759" />
<Atom class="CE3P" epsilon="0.7702744000000001" sigma="0.30495463121943817" />
<Atom class="PR3P" epsilon="0.7627432" sigma="0.2956180126533274" />
<Atom class="ND3P" epsilon="0.7497728" sigma="0.2886333667031071" />
<Atom class="PM3P" epsilon="0.74266" sigma="0.29527947114043407" />
<Atom class="SM3P" epsilon="0.7351288" sigma="0.2791542043420939" />
<Atom class="EU3P" epsilon="0.728016" sigma="0.2713677495455473" />
<Atom class="GD3P" epsilon="0.7209032000000001" sigma="0.2681605141602421" />
<Atom class="TB3P" epsilon="0.7083512000000001" sigma="0.2628151218514001" />
<Atom class="DY3P" epsilon="0.6999832" sigma="0.2573628216963812" />
<Atom class="HO3P" epsilon="0.6928704" sigma="0.247794569463554" />
<Atom class="ER3P" epsilon="0.6845024" sigma="0.24362516346265717" />
<Atom class="TM3P" epsilon="0.6778080000000001" sigma="0.24029320225681233" />
<Atom class="YB3P" epsilon="0.6711136" sigma="0.23077840394707347" />
<Atom class="LU3P" epsilon="0.6644192" sigma="0.2407564695902453" />
<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.35093300000000005" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.477963424" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024/tip3p-pme-f.xml 0 → 100644
View file @ be646878
<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str" md5hash="2a6cb5826fd2c30b3430fa8b04f34ec8" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str</Source>
<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-f">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="TP3F-OH2" />
<Type class="HT" element="H" mass="1.008" name="TP3F-H1" />
<Type class="HT" element="H" mass="1.008" name="TP3F-H2" />
<Type class="OX" element="O" mass="15.9994" name="OH-O1" />
<Type class="HX" element="H" mass="1.008" name="OH-H1" />
<Type class="LIT" element="Li" mass="6.941" name="LIT-LIT" />
<Type class="SOD" element="Na" mass="22.98977" name="SOD-SOD" />
<Type class="MG" element="Mg" mass="24.305" name="MG-MG" />
<Type class="POT" element="K" mass="39.0983" name="POT-POT" />
<Type class="CAL" element="Ca" mass="40.08" name="CAL-CAL" />
<Type class="RUB" element="Rb" mass="85.4678" name="RUB-RUB" />
<Type class="CES" element="Cs" mass="132.90545" name="CES-CES" />
<Type class="BAR" element="Ba" mass="137.327" name="BAR-BAR" />
<Type class="ZN" element="Zn" mass="65.37" name="ZN2-ZN" />
<Type class="CAD" element="Cd" mass="112.411" name="CD2-CD" />
<Type class="CLA" element="Cl" mass="35.45" name="CLA-CLA" />
<Type class="CU1P" element="Cu" mass="63.546" name="CU1P-CU1P" />
<Type class="AG1P" element="Ag" mass="107.87" name="AG1P-AG1P" />
<Type class="AU1P" element="Au" mass="196.97" name="AU1P-AU1P" />
<Type class="TI1P" element="Ti" mass="47.867" name="TI1P-TI1P" />
<Type class="BE2P" element="Be" mass="9.0122" name="BE2P-BE2P" />
<Type class="SR2P" element="Sr" mass="87.62" name="SR2P-SR2P" />
<Type class="RA2P" element="Ra" mass="226.03" name="RA2P-RA2P" />
<Type class="V2P" element="V" mass="50.942" name="V2P-V2P" />
<Type class="CR2P" element="Cr" mass="51.996" name="CR2P-CR2P" />
<Type class="MN2P" element="Mn" mass="54.938" name="MN2P-MN2P" />
<Type class="FE2P" element="Fe" mass="55.854" name="FE2P-FE2P" />
<Type class="CO2P" element="Co" mass="58.933" name="CO2P-CO2P" />
<Type class="NI2P" element="Ni" mass="58.693" name="NI2P-NI2P" />
<Type class="CU2P" element="Cu" mass="63.546" name="CU2P-CU2P" />
<Type class="PD2P" element="Pd" mass="106.42" name="PD2P-PD2P" />
<Type class="AG2P" element="Ag" mass="107.87" name="AG2P-AG2P" />
<Type class="SN2P" element="Sn" mass="118.71" name="SN2P-SN2P" />
<Type class="PT2P" element="Pt" mass="195.08" name="PT2P-PT2P" />
<Type class="HG2P" element="Hg" mass="200.59" name="HG2P-HG2P" />
<Type class="PB2P" element="Pb" mass="207.2" name="PB2P-PB2P" />
<Type class="SM2P" element="Sm" mass="150.36" name="SM2P-SM2P" />
<Type class="EU2P" element="Eu" mass="151.96" name="EU2P-EU2P" />
<Type class="YB2P" element="Yb" mass="173.05" name="YB2P-YB2P" />
<Type class="AL3P" element="Al" mass="26.982" name="AL3P-AL3P" />
<Type class="SC3P" element="Sc" mass="44.956" name="SC3P-SC3P" />
<Type class="Y3P" element="Y" mass="88.906" name="Y3P-Y3P" />
<Type class="LA3P" element="La" mass="138.91" name="LA3P-LA3P" />
<Type class="CE3P" element="Ce" mass="140.12" name="CE3P-CE3P" />
<Type class="PR3P" element="Pr" mass="140.91" name="PR3P-PR3P" />
<Type class="ND3P" element="Nd" mass="144.24" name="ND3P-ND3P" />
<Type class="PM3P" element="Pm" mass="144.91" name="PM3P-PM3P" />
<Type class="SM3P" element="Sm" mass="150.36" name="SM3P-SM3P" />
<Type class="EU3P" element="Eu" mass="151.96" name="EU3P-EU3P" />
<Type class="GD3P" element="Gd" mass="157.25" name="GD3P-GD3P" />
<Type class="TB3P" element="Tb" mass="158.93" name="TB3P-TB3P" />
<Type class="DY3P" element="Dy" mass="162.5" name="DY3P-DY3P" />
<Type class="HO3P" element="Ho" mass="164.93" name="HO3P-HO3P" />
<Type class="ER3P" element="Er" mass="167.28" name="ER3P-ER3P" />
<Type class="YB3P" element="Yb" mass="173.05" name="YB3P-YB3P" />
<Type class="LU3P" element="Lu" mass="174.97" name="LU3P-LU3P" />
<Type class="U3P" element="U" mass="238.03" name="U3P-U3P" />
<Type class="PU3P" element="Pu" mass="244.06" name="PU3P-PU3P" />
<Type class="TI3P" element="Ti" mass="47.867" name="TI3P-TI3P" />
<Type class="V3P" element="V" mass="50.942" name="V3P-V3P" />
<Type class="CR3P" element="Cr" mass="51.996" name="CR3P-CR3P" />
<Type class="MN3P" element="Mn" mass="54.938" name="MN3P-MN3P" />
<Type class="FE3P" element="Fe" mass="55.854" name="FE3P-FE3P" />
<Type class="CO3P" element="Co" mass="58.933" name="CO3P-CO3P" />
<Type class="GA3P" element="Ga" mass="69.723" name="GA3P-GA3P" />
<Type class="RH3P" element="Rh" mass="102.91" name="RH3P-RH3P" />
<Type class="IN3P" element="In" mass="114.82" name="IN3P-IN3P" />
<Type class="AU3P" element="Au" mass="196.97" name="AU3P-AU3P" />
<Type class="TL3P" element="Tl" mass="204.38" name="TL3P-TL3P" />
<Type class="BI3P" element="Bi" mass="208.98" name="BI3P-BI3P" />
</AtomTypes>
<Residues>
<Residue name="TP3F">
<Atom charge="-0.83" name="OH2" type="TP3F-OH2" />
<Atom charge="0.415" name="H1" type="TP3F-H1" />
<Atom charge="0.415" name="H2" type="TP3F-H2" />
<Bond atomName1="OH2" atomName2="H1" />
<Bond atomName1="OH2" atomName2="H2" />
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OH-O1" />
<Atom charge="0.32" name="H1" type="OH-H1" />
<Bond atomName1="O1" atomName2="H1" />
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT-LIT" />
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD-SOD" />
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG-MG" />
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT-POT" />
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL-CAL" />
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB-RUB" />
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES-CES" />
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR-BAR" />
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN2-ZN" />
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CD2-CD" />
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA-CLA" />
</Residue>
<Residue name="CU1P">
<Atom charge="1.0" name="CU1P" type="CU1P-CU1P" />
</Residue>
<Residue name="AG1P">
<Atom charge="1.0" name="AG1P" type="AG1P-AG1P" />
</Residue>
<Residue name="AU1P">
<Atom charge="1.0" name="AU1P" type="AU1P-AU1P" />
</Residue>
<Residue name="TI1P">
<Atom charge="1.0" name="TI1P" type="TI1P-TI1P" />
</Residue>
<Residue name="BE2P">
<Atom charge="2.0" name="BE2P" type="BE2P-BE2P" />
</Residue>
<Residue name="SR2P">
<Atom charge="2.0" name="SR2P" type="SR2P-SR2P" />
</Residue>
<Residue name="RA2P">
<Atom charge="2.0" name="RA2P" type="RA2P-RA2P" />
</Residue>
<Residue name="V2P">
<Atom charge="2.0" name="V2P" type="V2P-V2P" />
</Residue>
<Residue name="CR2P">
<Atom charge="2.0" name="CR2P" type="CR2P-CR2P" />
</Residue>
<Residue name="MN2P">
<Atom charge="2.0" name="MN2P" type="MN2P-MN2P" />
</Residue>
<Residue name="FE2P">
<Atom charge="2.0" name="FE2P" type="FE2P-FE2P" />
</Residue>
<Residue name="CO2P">
<Atom charge="2.0" name="CO2P" type="CO2P-CO2P" />
</Residue>
<Residue name="NI2P">
<Atom charge="2.0" name="NI2P" type="NI2P-NI2P" />
</Residue>
<Residue name="CU2P">
<Atom charge="2.0" name="CU2P" type="CU2P-CU2P" />
</Residue>
<Residue name="PD2P">
<Atom charge="2.0" name="PD2P" type="PD2P-PD2P" />
</Residue>
<Residue name="AG2P">
<Atom charge="2.0" name="AG2P" type="AG2P-AG2P" />
</Residue>
<Residue name="SN2P">
<Atom charge="2.0" name="SN2P" type="SN2P-SN2P" />
</Residue>
<Residue name="PT2P">
<Atom charge="2.0" name="PT2P" type="PT2P-PT2P" />
</Residue>
<Residue name="HG2P">
<Atom charge="2.0" name="HG2P" type="HG2P-HG2P" />
</Residue>
<Residue name="PB2P">
<Atom charge="2.0" name="PB2P" type="PB2P-PB2P" />
</Residue>
<Residue name="SM2P">
<Atom charge="2.0" name="SM2P" type="SM2P-SM2P" />
</Residue>
<Residue name="EU2P">
<Atom charge="2.0" name="EU2P" type="EU2P-EU2P" />
</Residue>
<Residue name="YB2P">
<Atom charge="2.0" name="YB2P" type="YB2P-YB2P" />
</Residue>
<Residue name="AL3P">
<Atom charge="3.0" name="AL3P" type="AL3P-AL3P" />
</Residue>
<Residue name="SC3P">
<Atom charge="3.0" name="SC3P" type="SC3P-SC3P" />
</Residue>
<Residue name="Y3P">
<Atom charge="3.0" name="Y3P" type="Y3P-Y3P" />
</Residue>
<Residue name="LA3P">
<Atom charge="3.0" name="LA3P" type="LA3P-LA3P" />
</Residue>
<Residue name="CE3P">
<Atom charge="3.0" name="CE3P" type="CE3P-CE3P" />
</Residue>
<Residue name="PR3P">
<Atom charge="3.0" name="PR3P" type="PR3P-PR3P" />
</Residue>
<Residue name="ND3P">
<Atom charge="3.0" name="ND3P" type="ND3P-ND3P" />
</Residue>
<Residue name="PM3P">
<Atom charge="3.0" name="PM3P" type="PM3P-PM3P" />
</Residue>
<Residue name="SM3P">
<Atom charge="3.0" name="SM3P" type="SM3P-SM3P" />
</Residue>
<Residue name="EU3P">
<Atom charge="3.0" name="EU3P" type="EU3P-EU3P" />
</Residue>
<Residue name="GD3P">
<Atom charge="3.0" name="GD3P" type="GD3P-GD3P" />
</Residue>
<Residue name="TB3P">
<Atom charge="3.0" name="TB3P" type="TB3P-TB3P" />
</Residue>
<Residue name="DY3P">
<Atom charge="3.0" name="DY3P" type="DY3P-DY3P" />
</Residue>
<Residue name="HO3P">
<Atom charge="3.0" name="HO3P" type="HO3P-HO3P" />
</Residue>
<Residue name="ER3P">
<Atom charge="3.0" name="ER3P" type="ER3P-ER3P" />
</Residue>
<Residue name="YB3P">
<Atom charge="3.0" name="YB3P" type="YB3P-YB3P" />
</Residue>
<Residue name="LU3P">
<Atom charge="3.0" name="LU3P" type="LU3P-LU3P" />
</Residue>
<Residue name="U3P">
<Atom charge="3.0" name="U3P" type="U3P-U3P" />
</Residue>
<Residue name="PU3P">
<Atom charge="3.0" name="PU3P" type="PU3P-PU3P" />
</Residue>
<Residue name="TI3P">
<Atom charge="3.0" name="TI3P" type="TI3P-TI3P" />
</Residue>
<Residue name="V3P">
<Atom charge="3.0" name="V3P" type="V3P-V3P" />
</Residue>
<Residue name="CR3P">
<Atom charge="3.0" name="CR3P" type="CR3P-CR3P" />
</Residue>
<Residue name="MN3P">
<Atom charge="3.0" name="MN3P" type="MN3P-MN3P" />
</Residue>
<Residue name="FE3P">
<Atom charge="3.0" name="FE3P" type="FE3P-FE3P" />
</Residue>
<Residue name="CO3P">
<Atom charge="3.0" name="CO3P" type="CO3P-CO3P" />
</Residue>
<Residue name="GA3P">
<Atom charge="3.0" name="GA3P" type="GA3P-GA3P" />
</Residue>
<Residue name="RH3P">
<Atom charge="3.0" name="RH3P" type="RH3P-RH3P" />
</Residue>
<Residue name="IN3P">
<Atom charge="3.0" name="IN3P" type="IN3P-IN3P" />
</Residue>
<Residue name="AU3P">
<Atom charge="3.0" name="AU3P" type="AU3P-AU3P" />
</Residue>
<Residue name="TL3P">
<Atom charge="3.0" name="TL3P" type="TL3P-TL3P" />
</Residue>
<Residue name="BI3P">
<Atom charge="3.0" name="BI3P" type="BI3P-BI3P" />
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="HT" class2="HT" k="0.0" length="0.15139000000000002" />
<Bond class1="HT" class2="OT" k="376559.99999999994" length="0.09572000000000001" />
<Bond class1="OX" class2="HX" k="456055.99999999994" length="0.097" />
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" class1="HT" class2="OT" class3="HT" k="460.24" />
</HarmonicAngleForce>
<AmoebaUreyBradleyForce />
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge" />
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.0" sigma="1.0" />
<Atom class="OT" epsilon="0.0" sigma="1.0" />
<Atom class="OX" epsilon="0.0" sigma="1.0" />
<Atom class="LIT" epsilon="0.0" sigma="1.0" />
<Atom class="SOD" epsilon="0.0" sigma="1.0" />
<Atom class="MG" epsilon="0.0" sigma="1.0" />
<Atom class="POT" epsilon="0.0" sigma="1.0" />
<Atom class="CAL" epsilon="0.0" sigma="1.0" />
<Atom class="RUB" epsilon="0.0" sigma="1.0" />
<Atom class="CES" epsilon="0.0" sigma="1.0" />
<Atom class="BAR" epsilon="0.0" sigma="1.0" />
<Atom class="ZN" epsilon="0.0" sigma="1.0" />
<Atom class="CAD" epsilon="0.0" sigma="1.0" />
<Atom class="CLA" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.0" sigma="1.0" />
<Atom class="AG1P" epsilon="0.0" sigma="1.0" />
<Atom class="AU1P" epsilon="0.0" sigma="1.0" />
<Atom class="TI1P" epsilon="0.0" sigma="1.0" />
<Atom class="BE2P" epsilon="0.0" sigma="1.0" />
<Atom class="SR2P" epsilon="0.0" sigma="1.0" />
<Atom class="RA2P" epsilon="0.0" sigma="1.0" />
<Atom class="V2P" epsilon="0.0" sigma="1.0" />
<Atom class="CR2P" epsilon="0.0" sigma="1.0" />
<Atom class="MN2P" epsilon="0.0" sigma="1.0" />
<Atom class="FE2P" epsilon="0.0" sigma="1.0" />
<Atom class="CO2P" epsilon="0.0" sigma="1.0" />
<Atom class="NI2P" epsilon="0.0" sigma="1.0" />
<Atom class="CU2P" epsilon="0.0" sigma="1.0" />
<Atom class="PD2P" epsilon="0.0" sigma="1.0" />
<Atom class="AG2P" epsilon="0.0" sigma="1.0" />
<Atom class="SN2P" epsilon="0.0" sigma="1.0" />
<Atom class="PT2P" epsilon="0.0" sigma="1.0" />
<Atom class="HG2P" epsilon="0.0" sigma="1.0" />
<Atom class="PB2P" epsilon="0.0" sigma="1.0" />
<Atom class="SM2P" epsilon="0.0" sigma="1.0" />
<Atom class="EU2P" epsilon="0.0" sigma="1.0" />
<Atom class="YB2P" epsilon="0.0" sigma="1.0" />
<Atom class="AL3P" epsilon="0.0" sigma="1.0" />
<Atom class="SC3P" epsilon="0.0" sigma="1.0" />
<Atom class="Y3P" epsilon="0.0" sigma="1.0" />
<Atom class="LA3P" epsilon="0.0" sigma="1.0" />
<Atom class="CE3P" epsilon="0.0" sigma="1.0" />
<Atom class="PR3P" epsilon="0.0" sigma="1.0" />
<Atom class="ND3P" epsilon="0.0" sigma="1.0" />
<Atom class="PM3P" epsilon="0.0" sigma="1.0" />
<Atom class="SM3P" epsilon="0.0" sigma="1.0" />
<Atom class="EU3P" epsilon="0.0" sigma="1.0" />
<Atom class="GD3P" epsilon="0.0" sigma="1.0" />
<Atom class="TB3P" epsilon="0.0" sigma="1.0" />
<Atom class="DY3P" epsilon="0.0" sigma="1.0" />
<Atom class="HO3P" epsilon="0.0" sigma="1.0" />
<Atom class="ER3P" epsilon="0.0" sigma="1.0" />
<Atom class="TM3P" epsilon="0.0" sigma="1.0" />
<Atom class="YB3P" epsilon="0.0" sigma="1.0" />
<Atom class="LU3P" epsilon="0.0" sigma="1.0" />
<Atom class="U3P" epsilon="0.0" sigma="1.0" />
<Atom class="PU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TI3P" epsilon="0.0" sigma="1.0" />
<Atom class="V3P" epsilon="0.0" sigma="1.0" />
<Atom class="CR3P" epsilon="0.0" sigma="1.0" />
<Atom class="MN3P" epsilon="0.0" sigma="1.0" />
<Atom class="FE3P" epsilon="0.0" sigma="1.0" />
<Atom class="CO3P" epsilon="0.0" sigma="1.0" />
<Atom class="GA3P" epsilon="0.0" sigma="1.0" />
<Atom class="RH3P" epsilon="0.0" sigma="1.0" />
<Atom class="IN3P" epsilon="0.0" sigma="1.0" />
<Atom class="AU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TL3P" epsilon="0.0" sigma="1.0" />
<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="OT" epsilon="0.410032" sigma="0.3194050084276745" />
<Atom class="OX" epsilon="0.50208" sigma="0.30290556416771536" />
<Atom class="LIT" epsilon="0.00974872" sigma="0.23118821735741807" />
<Atom class="SOD" epsilon="0.1962296" sigma="0.2513670733232967" />
<Atom class="MG" epsilon="0.06276" sigma="0.2111429961992604" />
<Atom class="POT" epsilon="0.364008" sigma="0.3142645228240047" />
<Atom class="CAL" epsilon="0.50208" sigma="0.24357170953956878" />
<Atom class="RUB" epsilon="0.6276" sigma="0.3385415128933289" />
<Atom class="CES" epsilon="0.79496" sigma="0.37417746161894255" />
<Atom class="BAR" epsilon="0.6276" sigma="0.33675971545704825" />
<Atom class="ZN" epsilon="1.046" sigma="0.194215920554594" />
<Atom class="CAD" epsilon="0.50208" sigma="0.2417899121032881" />
<Atom class="CLA" epsilon="0.6276" sigma="0.4044680180357141" />
<Atom class="CU1P" epsilon="0.7748768" sigma="0.1535909390073945" />
<Atom class="AG1P" epsilon="1.2008079999999999" sigma="0.2163636626875628" />
<Atom class="AU1P" epsilon="1.4907592" sigma="0.11250269012676205" />
<Atom class="TI1P" epsilon="1.7016328" sigma="0.34401163102271065" />
<Atom class="BE2P" epsilon="0.4250944" sigma="0.007127189745122714" />
<Atom class="SR2P" epsilon="0.9572992" sigma="0.3306837861993312" />
<Atom class="RA2P" epsilon="1.2631496" sigma="0.37237784620829906" />
<Atom class="V2P" epsilon="0.6732056" sigma="0.1966569830422985" />
<Atom class="CR2P" epsilon="0.6974728" sigma="0.18872798445084948" />
<Atom class="MN2P" epsilon="0.7050040000000001" sigma="0.2144749574051053" />
<Atom class="FE2P" epsilon="0.667348" sigma="0.1924519410926761" />
<Atom class="CO2P" epsilon="0.6439176000000001" sigma="0.16527953018939576" />
<Atom class="NI2P" epsilon="0.5999856" sigma="0.13903365395298137" />
<Atom class="CU2P" epsilon="0.629692" sigma="0.129198132104712" />
<Atom class="PD2P" epsilon="0.7288528" sigma="0.16519044031758173" />
<Atom class="AG2P" epsilon="0.7752952" sigma="0.1869105510658432" />
<Atom class="SN2P" epsilon="0.7861736" sigma="0.29542201493533654" />
<Atom class="PT2P" epsilon="0.6824104" sigma="0.1420270736459329" />
<Atom class="HG2P" epsilon="0.8593936" sigma="0.2105728210196506" />
<Atom class="PB2P" epsilon="1.0016496000000001" sigma="0.3132399892981433" />
<Atom class="SM2P" epsilon="1.0242432" sigma="0.330790694045508" />
<Atom class="EU2P" epsilon="0.9907712000000001" sigma="0.3279220001730961" />
<Atom class="YB2P" epsilon="0.8593936" sigma="0.28669120749756116" />
<Atom class="AL3P" epsilon="0.44601440000000003" sigma="0.039377723341803" />
<Atom class="SC3P" epsilon="0.5899439999999999" sigma="0.19544536078562763" />
<Atom class="Y3P" epsilon="0.6928704" sigma="0.25183924964391113" />
<Atom class="LA3P" epsilon="0.7932864" sigma="0.3158592315294759" />
<Atom class="CE3P" epsilon="0.7702744000000001" sigma="0.30495463121943817" />
<Atom class="PR3P" epsilon="0.7627432" sigma="0.2956180126533274" />
<Atom class="ND3P" epsilon="0.7497728" sigma="0.2886333667031071" />
<Atom class="PM3P" epsilon="0.74266" sigma="0.29527947114043407" />
<Atom class="SM3P" epsilon="0.7351288" sigma="0.2791542043420939" />
<Atom class="EU3P" epsilon="0.728016" sigma="0.2713677495455473" />
<Atom class="GD3P" epsilon="0.7209032000000001" sigma="0.2681605141602421" />
<Atom class="TB3P" epsilon="0.7083512000000001" sigma="0.2628151218514001" />
<Atom class="DY3P" epsilon="0.6999832" sigma="0.2573628216963812" />
<Atom class="HO3P" epsilon="0.6928704" sigma="0.247794569463554" />
<Atom class="ER3P" epsilon="0.6845024" sigma="0.24362516346265717" />
<Atom class="TM3P" epsilon="0.6778080000000001" sigma="0.24029320225681233" />
<Atom class="YB3P" epsilon="0.6711136" sigma="0.23077840394707347" />
<Atom class="LU3P" epsilon="0.6644192" sigma="0.2407564695902453" />
<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.35093300000000005" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.477963424" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024/tip4p2005.xml 0 → 100644
View file @ be646878
<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip4p_2005.str" md5hash="e2932421df3f88ec82c5a7b9b6c8292c" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_tip4p_2005.str</Source>
<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="J.L.F. Abascal and C. Vega. A general purpose model for the condensed phases of water: TIP4P/2005 J. Chem. Phys. 123:234505, 2005." forcefield="tip4p-2005">J.L.F. Abascal and C. Vega. A general purpose model for the condensed phases of water: TIP4P/2005 J. Chem. Phys. 123:234505, 2005.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="TP45-OH2" />
<Type class="LP" mass="0.0" name="TP45-OM" />
<Type class="HT" element="H" mass="1.008" name="TP45-H1" />
<Type class="HT" element="H" mass="1.008" name="TP45-H2" />
<Type class="OX" element="O" mass="15.9994" name="OH-O1" />
<Type class="HX" element="H" mass="1.008" name="OH-H1" />
<Type class="LIT" element="Li" mass="6.941" name="LIT-LIT" />
<Type class="SOD" element="Na" mass="22.98977" name="SOD-SOD" />
<Type class="MG" element="Mg" mass="24.305" name="MG-MG" />
<Type class="POT" element="K" mass="39.0983" name="POT-POT" />
<Type class="CAL" element="Ca" mass="40.08" name="CAL-CAL" />
<Type class="RUB" element="Rb" mass="85.4678" name="RUB-RUB" />
<Type class="CES" element="Cs" mass="132.90545" name="CES-CES" />
<Type class="BAR" element="Ba" mass="137.327" name="BAR-BAR" />
<Type class="ZN" element="Zn" mass="65.37" name="ZN2-ZN" />
<Type class="CAD" element="Cd" mass="112.411" name="CD2-CD" />
<Type class="CLA" element="Cl" mass="35.45" name="CLA-CLA" />
<Type class="CU1P" element="Cu" mass="63.546" name="CU1P-CU1P" />
<Type class="AG1P" element="Ag" mass="107.87" name="AG1P-AG1P" />
<Type class="AU1P" element="Au" mass="196.97" name="AU1P-AU1P" />
<Type class="TI1P" element="Ti" mass="47.867" name="TI1P-TI1P" />
<Type class="BE2P" element="Be" mass="9.0122" name="BE2P-BE2P" />
<Type class="SR2P" element="Sr" mass="87.62" name="SR2P-SR2P" />
<Type class="RA2P" element="Ra" mass="226.03" name="RA2P-RA2P" />
<Type class="V2P" element="V" mass="50.942" name="V2P-V2P" />
<Type class="CR2P" element="Cr" mass="51.996" name="CR2P-CR2P" />
<Type class="MN2P" element="Mn" mass="54.938" name="MN2P-MN2P" />
<Type class="FE2P" element="Fe" mass="55.854" name="FE2P-FE2P" />
<Type class="CO2P" element="Co" mass="58.933" name="CO2P-CO2P" />
<Type class="NI2P" element="Ni" mass="58.693" name="NI2P-NI2P" />
<Type class="CU2P" element="Cu" mass="63.546" name="CU2P-CU2P" />
<Type class="PD2P" element="Pd" mass="106.42" name="PD2P-PD2P" />
<Type class="AG2P" element="Ag" mass="107.87" name="AG2P-AG2P" />
<Type class="SN2P" element="Sn" mass="118.71" name="SN2P-SN2P" />
<Type class="PT2P" element="Pt" mass="195.08" name="PT2P-PT2P" />
<Type class="HG2P" element="Hg" mass="200.59" name="HG2P-HG2P" />
<Type class="PB2P" element="Pb" mass="207.2" name="PB2P-PB2P" />
<Type class="SM2P" element="Sm" mass="150.36" name="SM2P-SM2P" />
<Type class="EU2P" element="Eu" mass="151.96" name="EU2P-EU2P" />
<Type class="YB2P" element="Yb" mass="173.05" name="YB2P-YB2P" />
<Type class="AL3P" element="Al" mass="26.982" name="AL3P-AL3P" />
<Type class="SC3P" element="Sc" mass="44.956" name="SC3P-SC3P" />
<Type class="Y3P" element="Y" mass="88.906" name="Y3P-Y3P" />
<Type class="LA3P" element="La" mass="138.91" name="LA3P-LA3P" />
<Type class="CE3P" element="Ce" mass="140.12" name="CE3P-CE3P" />
<Type class="PR3P" element="Pr" mass="140.91" name="PR3P-PR3P" />
<Type class="ND3P" element="Nd" mass="144.24" name="ND3P-ND3P" />
<Type class="PM3P" element="Pm" mass="144.91" name="PM3P-PM3P" />
<Type class="SM3P" element="Sm" mass="150.36" name="SM3P-SM3P" />
<Type class="EU3P" element="Eu" mass="151.96" name="EU3P-EU3P" />
<Type class="GD3P" element="Gd" mass="157.25" name="GD3P-GD3P" />
<Type class="TB3P" element="Tb" mass="158.93" name="TB3P-TB3P" />
<Type class="DY3P" element="Dy" mass="162.5" name="DY3P-DY3P" />
<Type class="HO3P" element="Ho" mass="164.93" name="HO3P-HO3P" />
<Type class="ER3P" element="Er" mass="167.28" name="ER3P-ER3P" />
<Type class="YB3P" element="Yb" mass="173.05" name="YB3P-YB3P" />
<Type class="LU3P" element="Lu" mass="174.97" name="LU3P-LU3P" />
<Type class="U3P" element="U" mass="238.03" name="U3P-U3P" />
<Type class="PU3P" element="Pu" mass="244.06" name="PU3P-PU3P" />
<Type class="TI3P" element="Ti" mass="47.867" name="TI3P-TI3P" />
<Type class="V3P" element="V" mass="50.942" name="V3P-V3P" />
<Type class="CR3P" element="Cr" mass="51.996" name="CR3P-CR3P" />
<Type class="MN3P" element="Mn" mass="54.938" name="MN3P-MN3P" />
<Type class="FE3P" element="Fe" mass="55.854" name="FE3P-FE3P" />
<Type class="CO3P" element="Co" mass="58.933" name="CO3P-CO3P" />
<Type class="GA3P" element="Ga" mass="69.723" name="GA3P-GA3P" />
<Type class="RH3P" element="Rh" mass="102.91" name="RH3P-RH3P" />
<Type class="IN3P" element="In" mass="114.82" name="IN3P-IN3P" />
<Type class="AU3P" element="Au" mass="196.97" name="AU3P-AU3P" />
<Type class="TL3P" element="Tl" mass="204.38" name="TL3P-TL3P" />
<Type class="BI3P" element="Bi" mass="208.98" name="BI3P-BI3P" />
</AtomTypes>
<Residues>
<Residue name="TP45">
<Atom charge="0.0" name="OH2" type="TP45-OH2" />
<Atom charge="-1.1128" name="OM" type="TP45-OM" />
<Atom charge="0.5564" name="H1" type="TP45-H1" />
<Atom charge="0.5564" name="H2" type="TP45-H2" />
<Bond atomName1="OH2" atomName2="H1" />
<Bond atomName1="OH2" atomName2="H2" />
<VirtualSite atomName1="OH2" atomName2="H2" atomName3="H1" p1="0.015459999999999998" p2="0" p3="0" siteName="OM" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1" />
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OH-O1" />
<Atom charge="0.32" name="H1" type="OH-H1" />
<Bond atomName1="O1" atomName2="H1" />
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT-LIT" />
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD-SOD" />
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG-MG" />
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT-POT" />
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL-CAL" />
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB-RUB" />
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES-CES" />
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR-BAR" />
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN2-ZN" />
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CD2-CD" />
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA-CLA" />
</Residue>
<Residue name="CU1P">
<Atom charge="1.0" name="CU1P" type="CU1P-CU1P" />
</Residue>
<Residue name="AG1P">
<Atom charge="1.0" name="AG1P" type="AG1P-AG1P" />
</Residue>
<Residue name="AU1P">
<Atom charge="1.0" name="AU1P" type="AU1P-AU1P" />
</Residue>
<Residue name="TI1P">
<Atom charge="1.0" name="TI1P" type="TI1P-TI1P" />
</Residue>
<Residue name="BE2P">
<Atom charge="2.0" name="BE2P" type="BE2P-BE2P" />
</Residue>
<Residue name="SR2P">
<Atom charge="2.0" name="SR2P" type="SR2P-SR2P" />
</Residue>
<Residue name="RA2P">
<Atom charge="2.0" name="RA2P" type="RA2P-RA2P" />
</Residue>
<Residue name="V2P">
<Atom charge="2.0" name="V2P" type="V2P-V2P" />
</Residue>
<Residue name="CR2P">
<Atom charge="2.0" name="CR2P" type="CR2P-CR2P" />
</Residue>
<Residue name="MN2P">
<Atom charge="2.0" name="MN2P" type="MN2P-MN2P" />
</Residue>
<Residue name="FE2P">
<Atom charge="2.0" name="FE2P" type="FE2P-FE2P" />
</Residue>
<Residue name="CO2P">
<Atom charge="2.0" name="CO2P" type="CO2P-CO2P" />
</Residue>
<Residue name="NI2P">
<Atom charge="2.0" name="NI2P" type="NI2P-NI2P" />
</Residue>
<Residue name="CU2P">
<Atom charge="2.0" name="CU2P" type="CU2P-CU2P" />
</Residue>
<Residue name="PD2P">
<Atom charge="2.0" name="PD2P" type="PD2P-PD2P" />
</Residue>
<Residue name="AG2P">
<Atom charge="2.0" name="AG2P" type="AG2P-AG2P" />
</Residue>
<Residue name="SN2P">
<Atom charge="2.0" name="SN2P" type="SN2P-SN2P" />
</Residue>
<Residue name="PT2P">
<Atom charge="2.0" name="PT2P" type="PT2P-PT2P" />
</Residue>
<Residue name="HG2P">
<Atom charge="2.0" name="HG2P" type="HG2P-HG2P" />
</Residue>
<Residue name="PB2P">
<Atom charge="2.0" name="PB2P" type="PB2P-PB2P" />
</Residue>
<Residue name="SM2P">
<Atom charge="2.0" name="SM2P" type="SM2P-SM2P" />
</Residue>
<Residue name="EU2P">
<Atom charge="2.0" name="EU2P" type="EU2P-EU2P" />
</Residue>
<Residue name="YB2P">
<Atom charge="2.0" name="YB2P" type="YB2P-YB2P" />
</Residue>
<Residue name="AL3P">
<Atom charge="3.0" name="AL3P" type="AL3P-AL3P" />
</Residue>
<Residue name="SC3P">
<Atom charge="3.0" name="SC3P" type="SC3P-SC3P" />
</Residue>
<Residue name="Y3P">
<Atom charge="3.0" name="Y3P" type="Y3P-Y3P" />
</Residue>
<Residue name="LA3P">
<Atom charge="3.0" name="LA3P" type="LA3P-LA3P" />
</Residue>
<Residue name="CE3P">
<Atom charge="3.0" name="CE3P" type="CE3P-CE3P" />
</Residue>
<Residue name="PR3P">
<Atom charge="3.0" name="PR3P" type="PR3P-PR3P" />
</Residue>
<Residue name="ND3P">
<Atom charge="3.0" name="ND3P" type="ND3P-ND3P" />
</Residue>
<Residue name="PM3P">
<Atom charge="3.0" name="PM3P" type="PM3P-PM3P" />
</Residue>
<Residue name="SM3P">
<Atom charge="3.0" name="SM3P" type="SM3P-SM3P" />
</Residue>
<Residue name="EU3P">
<Atom charge="3.0" name="EU3P" type="EU3P-EU3P" />
</Residue>
<Residue name="GD3P">
<Atom charge="3.0" name="GD3P" type="GD3P-GD3P" />
</Residue>
<Residue name="TB3P">
<Atom charge="3.0" name="TB3P" type="TB3P-TB3P" />
</Residue>
<Residue name="DY3P">
<Atom charge="3.0" name="DY3P" type="DY3P-DY3P" />
</Residue>
<Residue name="HO3P">
<Atom charge="3.0" name="HO3P" type="HO3P-HO3P" />
</Residue>
<Residue name="ER3P">
<Atom charge="3.0" name="ER3P" type="ER3P-ER3P" />
</Residue>
<Residue name="YB3P">
<Atom charge="3.0" name="YB3P" type="YB3P-YB3P" />
</Residue>
<Residue name="LU3P">
<Atom charge="3.0" name="LU3P" type="LU3P-LU3P" />
</Residue>
<Residue name="U3P">
<Atom charge="3.0" name="U3P" type="U3P-U3P" />
</Residue>
<Residue name="PU3P">
<Atom charge="3.0" name="PU3P" type="PU3P-PU3P" />
</Residue>
<Residue name="TI3P">
<Atom charge="3.0" name="TI3P" type="TI3P-TI3P" />
</Residue>
<Residue name="V3P">
<Atom charge="3.0" name="V3P" type="V3P-V3P" />
</Residue>
<Residue name="CR3P">
<Atom charge="3.0" name="CR3P" type="CR3P-CR3P" />
</Residue>
<Residue name="MN3P">
<Atom charge="3.0" name="MN3P" type="MN3P-MN3P" />
</Residue>
<Residue name="FE3P">
<Atom charge="3.0" name="FE3P" type="FE3P-FE3P" />
</Residue>
<Residue name="CO3P">
<Atom charge="3.0" name="CO3P" type="CO3P-CO3P" />
</Residue>
<Residue name="GA3P">
<Atom charge="3.0" name="GA3P" type="GA3P-GA3P" />
</Residue>
<Residue name="RH3P">
<Atom charge="3.0" name="RH3P" type="RH3P-RH3P" />
</Residue>
<Residue name="IN3P">
<Atom charge="3.0" name="IN3P" type="IN3P-IN3P" />
</Residue>
<Residue name="AU3P">
<Atom charge="3.0" name="AU3P" type="AU3P-AU3P" />
</Residue>
<Residue name="TL3P">
<Atom charge="3.0" name="TL3P" type="TL3P-TL3P" />
</Residue>
<Residue name="BI3P">
<Atom charge="3.0" name="BI3P" type="BI3P-BI3P" />
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="HT" class2="HT" k="0.0" length="0.15139000000000002" />
<Bond class1="HT" class2="OT" k="376559.99999999994" length="0.09572000000000001" />
<Bond class1="OX" class2="HX" k="456055.99999999994" length="0.097" />
<Bond class1="OT" class2="LP" k="0.0" length="0.015" />
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" class1="HT" class2="OT" class3="HT" k="460.24" />
</HarmonicAngleForce>
<AmoebaUreyBradleyForce />
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge" />
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.0" sigma="1.0" />
<Atom class="OT" epsilon="0.0" sigma="1.0" />
<Atom class="OX" epsilon="0.0" sigma="1.0" />
<Atom class="LIT" epsilon="0.0" sigma="1.0" />
<Atom class="SOD" epsilon="0.0" sigma="1.0" />
<Atom class="MG" epsilon="0.0" sigma="1.0" />
<Atom class="POT" epsilon="0.0" sigma="1.0" />
<Atom class="CAL" epsilon="0.0" sigma="1.0" />
<Atom class="RUB" epsilon="0.0" sigma="1.0" />
<Atom class="CES" epsilon="0.0" sigma="1.0" />
<Atom class="BAR" epsilon="0.0" sigma="1.0" />
<Atom class="ZN" epsilon="0.0" sigma="1.0" />
<Atom class="CAD" epsilon="0.0" sigma="1.0" />
<Atom class="CLA" epsilon="0.0" sigma="1.0" />
<Atom class="LP" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.0" sigma="1.0" />
<Atom class="AG1P" epsilon="0.0" sigma="1.0" />
<Atom class="AU1P" epsilon="0.0" sigma="1.0" />
<Atom class="TI1P" epsilon="0.0" sigma="1.0" />
<Atom class="BE2P" epsilon="0.0" sigma="1.0" />
<Atom class="SR2P" epsilon="0.0" sigma="1.0" />
<Atom class="RA2P" epsilon="0.0" sigma="1.0" />
<Atom class="V2P" epsilon="0.0" sigma="1.0" />
<Atom class="CR2P" epsilon="0.0" sigma="1.0" />
<Atom class="MN2P" epsilon="0.0" sigma="1.0" />
<Atom class="FE2P" epsilon="0.0" sigma="1.0" />
<Atom class="CO2P" epsilon="0.0" sigma="1.0" />
<Atom class="NI2P" epsilon="0.0" sigma="1.0" />
<Atom class="CU2P" epsilon="0.0" sigma="1.0" />
<Atom class="PD2P" epsilon="0.0" sigma="1.0" />
<Atom class="AG2P" epsilon="0.0" sigma="1.0" />
<Atom class="SN2P" epsilon="0.0" sigma="1.0" />
<Atom class="PT2P" epsilon="0.0" sigma="1.0" />
<Atom class="HG2P" epsilon="0.0" sigma="1.0" />
<Atom class="PB2P" epsilon="0.0" sigma="1.0" />
<Atom class="SM2P" epsilon="0.0" sigma="1.0" />
<Atom class="EU2P" epsilon="0.0" sigma="1.0" />
<Atom class="YB2P" epsilon="0.0" sigma="1.0" />
<Atom class="AL3P" epsilon="0.0" sigma="1.0" />
<Atom class="SC3P" epsilon="0.0" sigma="1.0" />
<Atom class="Y3P" epsilon="0.0" sigma="1.0" />
<Atom class="LA3P" epsilon="0.0" sigma="1.0" />
<Atom class="CE3P" epsilon="0.0" sigma="1.0" />
<Atom class="PR3P" epsilon="0.0" sigma="1.0" />
<Atom class="ND3P" epsilon="0.0" sigma="1.0" />
<Atom class="PM3P" epsilon="0.0" sigma="1.0" />
<Atom class="SM3P" epsilon="0.0" sigma="1.0" />
<Atom class="EU3P" epsilon="0.0" sigma="1.0" />
<Atom class="GD3P" epsilon="0.0" sigma="1.0" />
<Atom class="TB3P" epsilon="0.0" sigma="1.0" />
<Atom class="DY3P" epsilon="0.0" sigma="1.0" />
<Atom class="HO3P" epsilon="0.0" sigma="1.0" />
<Atom class="ER3P" epsilon="0.0" sigma="1.0" />
<Atom class="TM3P" epsilon="0.0" sigma="1.0" />
<Atom class="YB3P" epsilon="0.0" sigma="1.0" />
<Atom class="LU3P" epsilon="0.0" sigma="1.0" />
<Atom class="U3P" epsilon="0.0" sigma="1.0" />
<Atom class="PU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TI3P" epsilon="0.0" sigma="1.0" />
<Atom class="V3P" epsilon="0.0" sigma="1.0" />
<Atom class="CR3P" epsilon="0.0" sigma="1.0" />
<Atom class="MN3P" epsilon="0.0" sigma="1.0" />
<Atom class="FE3P" epsilon="0.0" sigma="1.0" />
<Atom class="CO3P" epsilon="0.0" sigma="1.0" />
<Atom class="GA3P" epsilon="0.0" sigma="1.0" />
<Atom class="RH3P" epsilon="0.0" sigma="1.0" />
<Atom class="IN3P" epsilon="0.0" sigma="1.0" />
<Atom class="AU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TL3P" epsilon="0.0" sigma="1.0" />
<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="OT" epsilon="0.7748768" sigma="0.3158414135551131" />
<Atom class="OX" epsilon="0.50208" sigma="0.30290556416771536" />
<Atom class="LIT" epsilon="0.00974872" sigma="0.23118821735741807" />
<Atom class="SOD" epsilon="0.1962296" sigma="0.2513670733232967" />
<Atom class="MG" epsilon="0.06276" sigma="0.2111429961992604" />
<Atom class="POT" epsilon="0.364008" sigma="0.3142645228240047" />
<Atom class="CAL" epsilon="0.50208" sigma="0.24357170953956878" />
<Atom class="RUB" epsilon="0.6276" sigma="0.3385415128933289" />
<Atom class="CES" epsilon="0.79496" sigma="0.37417746161894255" />
<Atom class="BAR" epsilon="0.6276" sigma="0.33675971545704825" />
<Atom class="ZN" epsilon="1.046" sigma="0.194215920554594" />
<Atom class="CAD" epsilon="0.50208" sigma="0.2417899121032881" />
<Atom class="CLA" epsilon="0.6276" sigma="0.4044680180357141" />
<Atom class="LP" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.7748768" sigma="0.1535909390073945" />
<Atom class="AG1P" epsilon="1.2008079999999999" sigma="0.2163636626875628" />
<Atom class="AU1P" epsilon="1.4907592" sigma="0.11250269012676205" />
<Atom class="TI1P" epsilon="1.7016328" sigma="0.34401163102271065" />
<Atom class="BE2P" epsilon="0.4250944" sigma="0.007127189745122714" />
<Atom class="SR2P" epsilon="0.9572992" sigma="0.3306837861993312" />
<Atom class="RA2P" epsilon="1.2631496" sigma="0.37237784620829906" />
<Atom class="V2P" epsilon="0.6732056" sigma="0.1966569830422985" />
<Atom class="CR2P" epsilon="0.6974728" sigma="0.18872798445084948" />
<Atom class="MN2P" epsilon="0.7050040000000001" sigma="0.2144749574051053" />
<Atom class="FE2P" epsilon="0.667348" sigma="0.1924519410926761" />
<Atom class="CO2P" epsilon="0.6439176000000001" sigma="0.16527953018939576" />
<Atom class="NI2P" epsilon="0.5999856" sigma="0.13903365395298137" />
<Atom class="CU2P" epsilon="0.629692" sigma="0.129198132104712" />
<Atom class="PD2P" epsilon="0.7288528" sigma="0.16519044031758173" />
<Atom class="AG2P" epsilon="0.7752952" sigma="0.1869105510658432" />
<Atom class="SN2P" epsilon="0.7861736" sigma="0.29542201493533654" />
<Atom class="PT2P" epsilon="0.6824104" sigma="0.1420270736459329" />
<Atom class="HG2P" epsilon="0.8593936" sigma="0.2105728210196506" />
<Atom class="PB2P" epsilon="1.0016496000000001" sigma="0.3132399892981433" />
<Atom class="SM2P" epsilon="1.0242432" sigma="0.330790694045508" />
<Atom class="EU2P" epsilon="0.9907712000000001" sigma="0.3279220001730961" />
<Atom class="YB2P" epsilon="0.8593936" sigma="0.28669120749756116" />
<Atom class="AL3P" epsilon="0.44601440000000003" sigma="0.039377723341803" />
<Atom class="SC3P" epsilon="0.5899439999999999" sigma="0.19544536078562763" />
<Atom class="Y3P" epsilon="0.6928704" sigma="0.25183924964391113" />
<Atom class="LA3P" epsilon="0.7932864" sigma="0.3158592315294759" />
<Atom class="CE3P" epsilon="0.7702744000000001" sigma="0.30495463121943817" />
<Atom class="PR3P" epsilon="0.7627432" sigma="0.2956180126533274" />
<Atom class="ND3P" epsilon="0.7497728" sigma="0.2886333667031071" />
<Atom class="PM3P" epsilon="0.74266" sigma="0.29527947114043407" />
<Atom class="SM3P" epsilon="0.7351288" sigma="0.2791542043420939" />
<Atom class="EU3P" epsilon="0.728016" sigma="0.2713677495455473" />
<Atom class="GD3P" epsilon="0.7209032000000001" sigma="0.2681605141602421" />
<Atom class="TB3P" epsilon="0.7083512000000001" sigma="0.2628151218514001" />
<Atom class="DY3P" epsilon="0.6999832" sigma="0.2573628216963812" />
<Atom class="HO3P" epsilon="0.6928704" sigma="0.247794569463554" />
<Atom class="ER3P" epsilon="0.6845024" sigma="0.24362516346265717" />
<Atom class="TM3P" epsilon="0.6778080000000001" sigma="0.24029320225681233" />
<Atom class="YB3P" epsilon="0.6711136" sigma="0.23077840394707347" />
<Atom class="LU3P" epsilon="0.6644192" sigma="0.2407564695902453" />
<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.35093300000000005" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.477963424" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024/tip4pew.xml 0 → 100644
View file @ be646878
<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
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<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="H.W. Horn; W.C Swope; J.W. Pitera; J.D. Madura; T.J. Dick; G.L. Hura; T. Head-Gordon. J. Chem. Phys. 120:9665-9678, 2004." forcefield="tip4p-ew">H.W. Horn; W.C Swope; J.W. Pitera; J.D. Madura; T.J. Dick; G.L. Hura; T. Head-Gordon. J. Chem. Phys. 120:9665-9678, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
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<Atom class="IN3P" epsilon="0.0" sigma="1.0" />
<Atom class="AU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TL3P" epsilon="0.0" sigma="1.0" />
<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="OT" epsilon="0.680946" sigma="0.31642940670908576" />
<Atom class="OX" epsilon="0.50208" sigma="0.30290556416771536" />
<Atom class="LIT" epsilon="0.00974872" sigma="0.23118821735741807" />
<Atom class="SOD" epsilon="0.1962296" sigma="0.2513670733232967" />
<Atom class="MG" epsilon="0.06276" sigma="0.2111429961992604" />
<Atom class="POT" epsilon="0.364008" sigma="0.3142645228240047" />
<Atom class="CAL" epsilon="0.50208" sigma="0.24357170953956878" />
<Atom class="RUB" epsilon="0.6276" sigma="0.3385415128933289" />
<Atom class="CES" epsilon="0.79496" sigma="0.37417746161894255" />
<Atom class="BAR" epsilon="0.6276" sigma="0.33675971545704825" />
<Atom class="ZN" epsilon="1.046" sigma="0.194215920554594" />
<Atom class="CAD" epsilon="0.50208" sigma="0.2417899121032881" />
<Atom class="CLA" epsilon="0.6276" sigma="0.4044680180357141" />
<Atom class="LP" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.7748768" sigma="0.1535909390073945" />
<Atom class="AG1P" epsilon="1.2008079999999999" sigma="0.2163636626875628" />
<Atom class="AU1P" epsilon="1.4907592" sigma="0.11250269012676205" />
<Atom class="TI1P" epsilon="1.7016328" sigma="0.34401163102271065" />
<Atom class="BE2P" epsilon="0.4250944" sigma="0.007127189745122714" />
<Atom class="SR2P" epsilon="0.9572992" sigma="0.3306837861993312" />
<Atom class="RA2P" epsilon="1.2631496" sigma="0.37237784620829906" />
<Atom class="V2P" epsilon="0.6732056" sigma="0.1966569830422985" />
<Atom class="CR2P" epsilon="0.6974728" sigma="0.18872798445084948" />
<Atom class="MN2P" epsilon="0.7050040000000001" sigma="0.2144749574051053" />
<Atom class="FE2P" epsilon="0.667348" sigma="0.1924519410926761" />
<Atom class="CO2P" epsilon="0.6439176000000001" sigma="0.16527953018939576" />
<Atom class="NI2P" epsilon="0.5999856" sigma="0.13903365395298137" />
<Atom class="CU2P" epsilon="0.629692" sigma="0.129198132104712" />
<Atom class="PD2P" epsilon="0.7288528" sigma="0.16519044031758173" />
<Atom class="AG2P" epsilon="0.7752952" sigma="0.1869105510658432" />
<Atom class="SN2P" epsilon="0.7861736" sigma="0.29542201493533654" />
<Atom class="PT2P" epsilon="0.6824104" sigma="0.1420270736459329" />
<Atom class="HG2P" epsilon="0.8593936" sigma="0.2105728210196506" />
<Atom class="PB2P" epsilon="1.0016496000000001" sigma="0.3132399892981433" />
<Atom class="SM2P" epsilon="1.0242432" sigma="0.330790694045508" />
<Atom class="EU2P" epsilon="0.9907712000000001" sigma="0.3279220001730961" />
<Atom class="YB2P" epsilon="0.8593936" sigma="0.28669120749756116" />
<Atom class="AL3P" epsilon="0.44601440000000003" sigma="0.039377723341803" />
<Atom class="SC3P" epsilon="0.5899439999999999" sigma="0.19544536078562763" />
<Atom class="Y3P" epsilon="0.6928704" sigma="0.25183924964391113" />
<Atom class="LA3P" epsilon="0.7932864" sigma="0.3158592315294759" />
<Atom class="CE3P" epsilon="0.7702744000000001" sigma="0.30495463121943817" />
<Atom class="PR3P" epsilon="0.7627432" sigma="0.2956180126533274" />
<Atom class="ND3P" epsilon="0.7497728" sigma="0.2886333667031071" />
<Atom class="PM3P" epsilon="0.74266" sigma="0.29527947114043407" />
<Atom class="SM3P" epsilon="0.7351288" sigma="0.2791542043420939" />
<Atom class="EU3P" epsilon="0.728016" sigma="0.2713677495455473" />
<Atom class="GD3P" epsilon="0.7209032000000001" sigma="0.2681605141602421" />
<Atom class="TB3P" epsilon="0.7083512000000001" sigma="0.2628151218514001" />
<Atom class="DY3P" epsilon="0.6999832" sigma="0.2573628216963812" />
<Atom class="HO3P" epsilon="0.6928704" sigma="0.247794569463554" />
<Atom class="ER3P" epsilon="0.6845024" sigma="0.24362516346265717" />
<Atom class="TM3P" epsilon="0.6778080000000001" sigma="0.24029320225681233" />
<Atom class="YB3P" epsilon="0.6711136" sigma="0.23077840394707347" />
<Atom class="LU3P" epsilon="0.6644192" sigma="0.2407564695902453" />
<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.35093300000000005" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.477963424" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024/tip5p.xml 0 → 100644
View file @ be646878
<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip5p.str" md5hash="9c77ba3236c2f10e5474bcbda612a486" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_tip5p.str</Source>
<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="M.W. Mahoney and W.L. Jorgensen. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem Phys. 112:8910-8922, 2000." forcefield="tip5p">M.W. Mahoney and W.L. Jorgensen. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem Phys. 112:8910-8922, 2000.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="TIP5-OH2" />
<Type class="HT" element="H" mass="1.008" name="TIP5-H1" />
<Type class="HT" element="H" mass="1.008" name="TIP5-H2" />
<Type class="LP" mass="0.0" name="TIP5-LP1" />
<Type class="LP" mass="0.0" name="TIP5-LP2" />
<Type class="OX" element="O" mass="15.9994" name="OH-O1" />
<Type class="HX" element="H" mass="1.008" name="OH-H1" />
<Type class="LIT" element="Li" mass="6.941" name="LIT-LIT" />
<Type class="SOD" element="Na" mass="22.98977" name="SOD-SOD" />
<Type class="MG" element="Mg" mass="24.305" name="MG-MG" />
<Type class="POT" element="K" mass="39.0983" name="POT-POT" />
<Type class="CAL" element="Ca" mass="40.08" name="CAL-CAL" />
<Type class="RUB" element="Rb" mass="85.4678" name="RUB-RUB" />
<Type class="CES" element="Cs" mass="132.90545" name="CES-CES" />
<Type class="BAR" element="Ba" mass="137.327" name="BAR-BAR" />
<Type class="ZN" element="Zn" mass="65.37" name="ZN2-ZN" />
<Type class="CAD" element="Cd" mass="112.411" name="CD2-CD" />
<Type class="CLA" element="Cl" mass="35.45" name="CLA-CLA" />
<Type class="CU1P" element="Cu" mass="63.546" name="CU1P-CU1P" />
<Type class="AG1P" element="Ag" mass="107.87" name="AG1P-AG1P" />
<Type class="AU1P" element="Au" mass="196.97" name="AU1P-AU1P" />
<Type class="TI1P" element="Ti" mass="47.867" name="TI1P-TI1P" />
<Type class="BE2P" element="Be" mass="9.0122" name="BE2P-BE2P" />
<Type class="SR2P" element="Sr" mass="87.62" name="SR2P-SR2P" />
<Type class="RA2P" element="Ra" mass="226.03" name="RA2P-RA2P" />
<Type class="V2P" element="V" mass="50.942" name="V2P-V2P" />
<Type class="CR2P" element="Cr" mass="51.996" name="CR2P-CR2P" />
<Type class="MN2P" element="Mn" mass="54.938" name="MN2P-MN2P" />
<Type class="FE2P" element="Fe" mass="55.854" name="FE2P-FE2P" />
<Type class="CO2P" element="Co" mass="58.933" name="CO2P-CO2P" />
<Type class="NI2P" element="Ni" mass="58.693" name="NI2P-NI2P" />
<Type class="CU2P" element="Cu" mass="63.546" name="CU2P-CU2P" />
<Type class="PD2P" element="Pd" mass="106.42" name="PD2P-PD2P" />
<Type class="AG2P" element="Ag" mass="107.87" name="AG2P-AG2P" />
<Type class="SN2P" element="Sn" mass="118.71" name="SN2P-SN2P" />
<Type class="PT2P" element="Pt" mass="195.08" name="PT2P-PT2P" />
<Type class="HG2P" element="Hg" mass="200.59" name="HG2P-HG2P" />
<Type class="PB2P" element="Pb" mass="207.2" name="PB2P-PB2P" />
<Type class="SM2P" element="Sm" mass="150.36" name="SM2P-SM2P" />
<Type class="EU2P" element="Eu" mass="151.96" name="EU2P-EU2P" />
<Type class="YB2P" element="Yb" mass="173.05" name="YB2P-YB2P" />
<Type class="AL3P" element="Al" mass="26.982" name="AL3P-AL3P" />
<Type class="SC3P" element="Sc" mass="44.956" name="SC3P-SC3P" />
<Type class="Y3P" element="Y" mass="88.906" name="Y3P-Y3P" />
<Type class="LA3P" element="La" mass="138.91" name="LA3P-LA3P" />
<Type class="CE3P" element="Ce" mass="140.12" name="CE3P-CE3P" />
<Type class="PR3P" element="Pr" mass="140.91" name="PR3P-PR3P" />
<Type class="ND3P" element="Nd" mass="144.24" name="ND3P-ND3P" />
<Type class="PM3P" element="Pm" mass="144.91" name="PM3P-PM3P" />
<Type class="SM3P" element="Sm" mass="150.36" name="SM3P-SM3P" />
<Type class="EU3P" element="Eu" mass="151.96" name="EU3P-EU3P" />
<Type class="GD3P" element="Gd" mass="157.25" name="GD3P-GD3P" />
<Type class="TB3P" element="Tb" mass="158.93" name="TB3P-TB3P" />
<Type class="DY3P" element="Dy" mass="162.5" name="DY3P-DY3P" />
<Type class="HO3P" element="Ho" mass="164.93" name="HO3P-HO3P" />
<Type class="ER3P" element="Er" mass="167.28" name="ER3P-ER3P" />
<Type class="YB3P" element="Yb" mass="173.05" name="YB3P-YB3P" />
<Type class="LU3P" element="Lu" mass="174.97" name="LU3P-LU3P" />
<Type class="U3P" element="U" mass="238.03" name="U3P-U3P" />
<Type class="PU3P" element="Pu" mass="244.06" name="PU3P-PU3P" />
<Type class="TI3P" element="Ti" mass="47.867" name="TI3P-TI3P" />
<Type class="V3P" element="V" mass="50.942" name="V3P-V3P" />
<Type class="CR3P" element="Cr" mass="51.996" name="CR3P-CR3P" />
<Type class="MN3P" element="Mn" mass="54.938" name="MN3P-MN3P" />
<Type class="FE3P" element="Fe" mass="55.854" name="FE3P-FE3P" />
<Type class="CO3P" element="Co" mass="58.933" name="CO3P-CO3P" />
<Type class="GA3P" element="Ga" mass="69.723" name="GA3P-GA3P" />
<Type class="RH3P" element="Rh" mass="102.91" name="RH3P-RH3P" />
<Type class="IN3P" element="In" mass="114.82" name="IN3P-IN3P" />
<Type class="AU3P" element="Au" mass="196.97" name="AU3P-AU3P" />
<Type class="TL3P" element="Tl" mass="204.38" name="TL3P-TL3P" />
<Type class="BI3P" element="Bi" mass="208.98" name="BI3P-BI3P" />
</AtomTypes>
<Residues>
<Residue name="TIP5">
<Atom charge="0.0" name="OH2" type="TIP5-OH2" />
<Atom charge="0.241" name="H1" type="TIP5-H1" />
<Atom charge="0.241" name="H2" type="TIP5-H2" />
<Atom charge="-0.241" name="LP1" type="TIP5-LP1" />
<Atom charge="-0.241" name="LP2" type="TIP5-LP2" />
<Bond atomName1="OH2" atomName2="H1" />
<Bond atomName1="OH2" atomName2="H2" />
<VirtualSite atomName1="OH2" atomName2="H2" atomName3="H1" p1="-0.04041512765608711" p2="0" p3="0.057154330164408206" siteName="LP1" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OH2" atomName2="H2" atomName3="H1" p1="-0.04041512765608711" p2="0" p3="-0.057154330164408206" siteName="LP2" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1" />
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OH-O1" />
<Atom charge="0.32" name="H1" type="OH-H1" />
<Bond atomName1="O1" atomName2="H1" />
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT-LIT" />
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD-SOD" />
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG-MG" />
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT-POT" />
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL-CAL" />
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB-RUB" />
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES-CES" />
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR-BAR" />
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN2-ZN" />
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CD2-CD" />
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA-CLA" />
</Residue>
<Residue name="CU1P">
<Atom charge="1.0" name="CU1P" type="CU1P-CU1P" />
</Residue>
<Residue name="AG1P">
<Atom charge="1.0" name="AG1P" type="AG1P-AG1P" />
</Residue>
<Residue name="AU1P">
<Atom charge="1.0" name="AU1P" type="AU1P-AU1P" />
</Residue>
<Residue name="TI1P">
<Atom charge="1.0" name="TI1P" type="TI1P-TI1P" />
</Residue>
<Residue name="BE2P">
<Atom charge="2.0" name="BE2P" type="BE2P-BE2P" />
</Residue>
<Residue name="SR2P">
<Atom charge="2.0" name="SR2P" type="SR2P-SR2P" />
</Residue>
<Residue name="RA2P">
<Atom charge="2.0" name="RA2P" type="RA2P-RA2P" />
</Residue>
<Residue name="V2P">
<Atom charge="2.0" name="V2P" type="V2P-V2P" />
</Residue>
<Residue name="CR2P">
<Atom charge="2.0" name="CR2P" type="CR2P-CR2P" />
</Residue>
<Residue name="MN2P">
<Atom charge="2.0" name="MN2P" type="MN2P-MN2P" />
</Residue>
<Residue name="FE2P">
<Atom charge="2.0" name="FE2P" type="FE2P-FE2P" />
</Residue>
<Residue name="CO2P">
<Atom charge="2.0" name="CO2P" type="CO2P-CO2P" />
</Residue>
<Residue name="NI2P">
<Atom charge="2.0" name="NI2P" type="NI2P-NI2P" />
</Residue>
<Residue name="CU2P">
<Atom charge="2.0" name="CU2P" type="CU2P-CU2P" />
</Residue>
<Residue name="PD2P">
<Atom charge="2.0" name="PD2P" type="PD2P-PD2P" />
</Residue>
<Residue name="AG2P">
<Atom charge="2.0" name="AG2P" type="AG2P-AG2P" />
</Residue>
<Residue name="SN2P">
<Atom charge="2.0" name="SN2P" type="SN2P-SN2P" />
</Residue>
<Residue name="PT2P">
<Atom charge="2.0" name="PT2P" type="PT2P-PT2P" />
</Residue>
<Residue name="HG2P">
<Atom charge="2.0" name="HG2P" type="HG2P-HG2P" />
</Residue>
<Residue name="PB2P">
<Atom charge="2.0" name="PB2P" type="PB2P-PB2P" />
</Residue>
<Residue name="SM2P">
<Atom charge="2.0" name="SM2P" type="SM2P-SM2P" />
</Residue>
<Residue name="EU2P">
<Atom charge="2.0" name="EU2P" type="EU2P-EU2P" />
</Residue>
<Residue name="YB2P">
<Atom charge="2.0" name="YB2P" type="YB2P-YB2P" />
</Residue>
<Residue name="AL3P">
<Atom charge="3.0" name="AL3P" type="AL3P-AL3P" />
</Residue>
<Residue name="SC3P">
<Atom charge="3.0" name="SC3P" type="SC3P-SC3P" />
</Residue>
<Residue name="Y3P">
<Atom charge="3.0" name="Y3P" type="Y3P-Y3P" />
</Residue>
<Residue name="LA3P">
<Atom charge="3.0" name="LA3P" type="LA3P-LA3P" />
</Residue>
<Residue name="CE3P">
<Atom charge="3.0" name="CE3P" type="CE3P-CE3P" />
</Residue>
<Residue name="PR3P">
<Atom charge="3.0" name="PR3P" type="PR3P-PR3P" />
</Residue>
<Residue name="ND3P">
<Atom charge="3.0" name="ND3P" type="ND3P-ND3P" />
</Residue>
<Residue name="PM3P">
<Atom charge="3.0" name="PM3P" type="PM3P-PM3P" />
</Residue>
<Residue name="SM3P">
<Atom charge="3.0" name="SM3P" type="SM3P-SM3P" />
</Residue>
<Residue name="EU3P">
<Atom charge="3.0" name="EU3P" type="EU3P-EU3P" />
</Residue>
<Residue name="GD3P">
<Atom charge="3.0" name="GD3P" type="GD3P-GD3P" />
</Residue>
<Residue name="TB3P">
<Atom charge="3.0" name="TB3P" type="TB3P-TB3P" />
</Residue>
<Residue name="DY3P">
<Atom charge="3.0" name="DY3P" type="DY3P-DY3P" />
</Residue>
<Residue name="HO3P">
<Atom charge="3.0" name="HO3P" type="HO3P-HO3P" />
</Residue>
<Residue name="ER3P">
<Atom charge="3.0" name="ER3P" type="ER3P-ER3P" />
</Residue>
<Residue name="YB3P">
<Atom charge="3.0" name="YB3P" type="YB3P-YB3P" />
</Residue>
<Residue name="LU3P">
<Atom charge="3.0" name="LU3P" type="LU3P-LU3P" />
</Residue>
<Residue name="U3P">
<Atom charge="3.0" name="U3P" type="U3P-U3P" />
</Residue>
<Residue name="PU3P">
<Atom charge="3.0" name="PU3P" type="PU3P-PU3P" />
</Residue>
<Residue name="TI3P">
<Atom charge="3.0" name="TI3P" type="TI3P-TI3P" />
</Residue>
<Residue name="V3P">
<Atom charge="3.0" name="V3P" type="V3P-V3P" />
</Residue>
<Residue name="CR3P">
<Atom charge="3.0" name="CR3P" type="CR3P-CR3P" />
</Residue>
<Residue name="MN3P">
<Atom charge="3.0" name="MN3P" type="MN3P-MN3P" />
</Residue>
<Residue name="FE3P">
<Atom charge="3.0" name="FE3P" type="FE3P-FE3P" />
</Residue>
<Residue name="CO3P">
<Atom charge="3.0" name="CO3P" type="CO3P-CO3P" />
</Residue>
<Residue name="GA3P">
<Atom charge="3.0" name="GA3P" type="GA3P-GA3P" />
</Residue>
<Residue name="RH3P">
<Atom charge="3.0" name="RH3P" type="RH3P-RH3P" />
</Residue>
<Residue name="IN3P">
<Atom charge="3.0" name="IN3P" type="IN3P-IN3P" />
</Residue>
<Residue name="AU3P">
<Atom charge="3.0" name="AU3P" type="AU3P-AU3P" />
</Residue>
<Residue name="TL3P">
<Atom charge="3.0" name="TL3P" type="TL3P-TL3P" />
</Residue>
<Residue name="BI3P">
<Atom charge="3.0" name="BI3P" type="BI3P-BI3P" />
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="HT" class2="HT" k="0.0" length="0.15139000000000002" />
<Bond class1="HT" class2="OT" k="376559.99999999994" length="0.09572000000000001" />
<Bond class1="OX" class2="HX" k="456055.99999999994" length="0.097" />
<Bond class1="OT" class2="LP" k="0.0" length="0.06999999999999999" />
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" class1="HT" class2="OT" class3="HT" k="460.24" />
</HarmonicAngleForce>
<AmoebaUreyBradleyForce />
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge" />
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.0" sigma="1.0" />
<Atom class="OT" epsilon="0.0" sigma="1.0" />
<Atom class="OX" epsilon="0.0" sigma="1.0" />
<Atom class="LIT" epsilon="0.0" sigma="1.0" />
<Atom class="SOD" epsilon="0.0" sigma="1.0" />
<Atom class="MG" epsilon="0.0" sigma="1.0" />
<Atom class="POT" epsilon="0.0" sigma="1.0" />
<Atom class="CAL" epsilon="0.0" sigma="1.0" />
<Atom class="RUB" epsilon="0.0" sigma="1.0" />
<Atom class="CES" epsilon="0.0" sigma="1.0" />
<Atom class="BAR" epsilon="0.0" sigma="1.0" />
<Atom class="ZN" epsilon="0.0" sigma="1.0" />
<Atom class="CAD" epsilon="0.0" sigma="1.0" />
<Atom class="CLA" epsilon="0.0" sigma="1.0" />
<Atom class="LP" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.0" sigma="1.0" />
<Atom class="AG1P" epsilon="0.0" sigma="1.0" />
<Atom class="AU1P" epsilon="0.0" sigma="1.0" />
<Atom class="TI1P" epsilon="0.0" sigma="1.0" />
<Atom class="BE2P" epsilon="0.0" sigma="1.0" />
<Atom class="SR2P" epsilon="0.0" sigma="1.0" />
<Atom class="RA2P" epsilon="0.0" sigma="1.0" />
<Atom class="V2P" epsilon="0.0" sigma="1.0" />
<Atom class="CR2P" epsilon="0.0" sigma="1.0" />
<Atom class="MN2P" epsilon="0.0" sigma="1.0" />
<Atom class="FE2P" epsilon="0.0" sigma="1.0" />
<Atom class="CO2P" epsilon="0.0" sigma="1.0" />
<Atom class="NI2P" epsilon="0.0" sigma="1.0" />
<Atom class="CU2P" epsilon="0.0" sigma="1.0" />
<Atom class="PD2P" epsilon="0.0" sigma="1.0" />
<Atom class="AG2P" epsilon="0.0" sigma="1.0" />
<Atom class="SN2P" epsilon="0.0" sigma="1.0" />
<Atom class="PT2P" epsilon="0.0" sigma="1.0" />
<Atom class="HG2P" epsilon="0.0" sigma="1.0" />
<Atom class="PB2P" epsilon="0.0" sigma="1.0" />
<Atom class="SM2P" epsilon="0.0" sigma="1.0" />
<Atom class="EU2P" epsilon="0.0" sigma="1.0" />
<Atom class="YB2P" epsilon="0.0" sigma="1.0" />
<Atom class="AL3P" epsilon="0.0" sigma="1.0" />
<Atom class="SC3P" epsilon="0.0" sigma="1.0" />
<Atom class="Y3P" epsilon="0.0" sigma="1.0" />
<Atom class="LA3P" epsilon="0.0" sigma="1.0" />
<Atom class="CE3P" epsilon="0.0" sigma="1.0" />
<Atom class="PR3P" epsilon="0.0" sigma="1.0" />
<Atom class="ND3P" epsilon="0.0" sigma="1.0" />
<Atom class="PM3P" epsilon="0.0" sigma="1.0" />
<Atom class="SM3P" epsilon="0.0" sigma="1.0" />
<Atom class="EU3P" epsilon="0.0" sigma="1.0" />
<Atom class="GD3P" epsilon="0.0" sigma="1.0" />
<Atom class="TB3P" epsilon="0.0" sigma="1.0" />
<Atom class="DY3P" epsilon="0.0" sigma="1.0" />
<Atom class="HO3P" epsilon="0.0" sigma="1.0" />
<Atom class="ER3P" epsilon="0.0" sigma="1.0" />
<Atom class="TM3P" epsilon="0.0" sigma="1.0" />
<Atom class="YB3P" epsilon="0.0" sigma="1.0" />
<Atom class="LU3P" epsilon="0.0" sigma="1.0" />
<Atom class="U3P" epsilon="0.0" sigma="1.0" />
<Atom class="PU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TI3P" epsilon="0.0" sigma="1.0" />
<Atom class="V3P" epsilon="0.0" sigma="1.0" />
<Atom class="CR3P" epsilon="0.0" sigma="1.0" />
<Atom class="MN3P" epsilon="0.0" sigma="1.0" />
<Atom class="FE3P" epsilon="0.0" sigma="1.0" />
<Atom class="CO3P" epsilon="0.0" sigma="1.0" />
<Atom class="GA3P" epsilon="0.0" sigma="1.0" />
<Atom class="RH3P" epsilon="0.0" sigma="1.0" />
<Atom class="IN3P" epsilon="0.0" sigma="1.0" />
<Atom class="AU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TL3P" epsilon="0.0" sigma="1.0" />
<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="OT" epsilon="0.66944" sigma="0.3119570951440212" />
<Atom class="OX" epsilon="0.50208" sigma="0.30290556416771536" />
<Atom class="LIT" epsilon="0.00974872" sigma="0.23118821735741807" />
<Atom class="SOD" epsilon="0.1962296" sigma="0.2513670733232967" />
<Atom class="MG" epsilon="0.06276" sigma="0.2111429961992604" />
<Atom class="POT" epsilon="0.364008" sigma="0.3142645228240047" />
<Atom class="CAL" epsilon="0.50208" sigma="0.24357170953956878" />
<Atom class="RUB" epsilon="0.6276" sigma="0.3385415128933289" />
<Atom class="CES" epsilon="0.79496" sigma="0.37417746161894255" />
<Atom class="BAR" epsilon="0.6276" sigma="0.33675971545704825" />
<Atom class="ZN" epsilon="1.046" sigma="0.194215920554594" />
<Atom class="CAD" epsilon="0.50208" sigma="0.2417899121032881" />
<Atom class="CLA" epsilon="0.6276" sigma="0.4044680180357141" />
<Atom class="LP" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.7748768" sigma="0.1535909390073945" />
<Atom class="AG1P" epsilon="1.2008079999999999" sigma="0.2163636626875628" />
<Atom class="AU1P" epsilon="1.4907592" sigma="0.11250269012676205" />
<Atom class="TI1P" epsilon="1.7016328" sigma="0.34401163102271065" />
<Atom class="BE2P" epsilon="0.4250944" sigma="0.007127189745122714" />
<Atom class="SR2P" epsilon="0.9572992" sigma="0.3306837861993312" />
<Atom class="RA2P" epsilon="1.2631496" sigma="0.37237784620829906" />
<Atom class="V2P" epsilon="0.6732056" sigma="0.1966569830422985" />
<Atom class="CR2P" epsilon="0.6974728" sigma="0.18872798445084948" />
<Atom class="MN2P" epsilon="0.7050040000000001" sigma="0.2144749574051053" />
<Atom class="FE2P" epsilon="0.667348" sigma="0.1924519410926761" />
<Atom class="CO2P" epsilon="0.6439176000000001" sigma="0.16527953018939576" />
<Atom class="NI2P" epsilon="0.5999856" sigma="0.13903365395298137" />
<Atom class="CU2P" epsilon="0.629692" sigma="0.129198132104712" />
<Atom class="PD2P" epsilon="0.7288528" sigma="0.16519044031758173" />
<Atom class="AG2P" epsilon="0.7752952" sigma="0.1869105510658432" />
<Atom class="SN2P" epsilon="0.7861736" sigma="0.29542201493533654" />
<Atom class="PT2P" epsilon="0.6824104" sigma="0.1420270736459329" />
<Atom class="HG2P" epsilon="0.8593936" sigma="0.2105728210196506" />
<Atom class="PB2P" epsilon="1.0016496000000001" sigma="0.3132399892981433" />
<Atom class="SM2P" epsilon="1.0242432" sigma="0.330790694045508" />
<Atom class="EU2P" epsilon="0.9907712000000001" sigma="0.3279220001730961" />
<Atom class="YB2P" epsilon="0.8593936" sigma="0.28669120749756116" />
<Atom class="AL3P" epsilon="0.44601440000000003" sigma="0.039377723341803" />
<Atom class="SC3P" epsilon="0.5899439999999999" sigma="0.19544536078562763" />
<Atom class="Y3P" epsilon="0.6928704" sigma="0.25183924964391113" />
<Atom class="LA3P" epsilon="0.7932864" sigma="0.3158592315294759" />
<Atom class="CE3P" epsilon="0.7702744000000001" sigma="0.30495463121943817" />
<Atom class="PR3P" epsilon="0.7627432" sigma="0.2956180126533274" />
<Atom class="ND3P" epsilon="0.7497728" sigma="0.2886333667031071" />
<Atom class="PM3P" epsilon="0.74266" sigma="0.29527947114043407" />
<Atom class="SM3P" epsilon="0.7351288" sigma="0.2791542043420939" />
<Atom class="EU3P" epsilon="0.728016" sigma="0.2713677495455473" />
<Atom class="GD3P" epsilon="0.7209032000000001" sigma="0.2681605141602421" />
<Atom class="TB3P" epsilon="0.7083512000000001" sigma="0.2628151218514001" />
<Atom class="DY3P" epsilon="0.6999832" sigma="0.2573628216963812" />
<Atom class="HO3P" epsilon="0.6928704" sigma="0.247794569463554" />
<Atom class="ER3P" epsilon="0.6845024" sigma="0.24362516346265717" />
<Atom class="TM3P" epsilon="0.6778080000000001" sigma="0.24029320225681233" />
<Atom class="YB3P" epsilon="0.6711136" sigma="0.23077840394707347" />
<Atom class="LU3P" epsilon="0.6644192" sigma="0.2407564695902453" />
<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.35093300000000005" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.477963424" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024/tip5pew.xml 0 → 100644
View file @ be646878
<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip5p_ew.str" md5hash="f12096ec0aa691de80983a34cc5cce5a" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_tip5p_ew.str</Source>
<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="Rick, S.W. A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. J Chem Phys 120: 6085-93, 2004." forcefield="tip5p-ew">Rick, S.W. A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. J Chem Phys 120: 6085-93, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="TP5E-OH2" />
<Type class="HT" element="H" mass="1.008" name="TP5E-H1" />
<Type class="HT" element="H" mass="1.008" name="TP5E-H2" />
<Type class="LP" mass="0.0" name="TP5E-LP1" />
<Type class="LP" mass="0.0" name="TP5E-LP2" />
<Type class="OX" element="O" mass="15.9994" name="OH-O1" />
<Type class="HX" element="H" mass="1.008" name="OH-H1" />
<Type class="LIT" element="Li" mass="6.941" name="LIT-LIT" />
<Type class="SOD" element="Na" mass="22.98977" name="SOD-SOD" />
<Type class="MG" element="Mg" mass="24.305" name="MG-MG" />
<Type class="POT" element="K" mass="39.0983" name="POT-POT" />
<Type class="CAL" element="Ca" mass="40.08" name="CAL-CAL" />
<Type class="RUB" element="Rb" mass="85.4678" name="RUB-RUB" />
<Type class="CES" element="Cs" mass="132.90545" name="CES-CES" />
<Type class="BAR" element="Ba" mass="137.327" name="BAR-BAR" />
<Type class="ZN" element="Zn" mass="65.37" name="ZN2-ZN" />
<Type class="CAD" element="Cd" mass="112.411" name="CD2-CD" />
<Type class="CLA" element="Cl" mass="35.45" name="CLA-CLA" />
<Type class="CU1P" element="Cu" mass="63.546" name="CU1P-CU1P" />
<Type class="AG1P" element="Ag" mass="107.87" name="AG1P-AG1P" />
<Type class="AU1P" element="Au" mass="196.97" name="AU1P-AU1P" />
<Type class="TI1P" element="Ti" mass="47.867" name="TI1P-TI1P" />
<Type class="BE2P" element="Be" mass="9.0122" name="BE2P-BE2P" />
<Type class="SR2P" element="Sr" mass="87.62" name="SR2P-SR2P" />
<Type class="RA2P" element="Ra" mass="226.03" name="RA2P-RA2P" />
<Type class="V2P" element="V" mass="50.942" name="V2P-V2P" />
<Type class="CR2P" element="Cr" mass="51.996" name="CR2P-CR2P" />
<Type class="MN2P" element="Mn" mass="54.938" name="MN2P-MN2P" />
<Type class="FE2P" element="Fe" mass="55.854" name="FE2P-FE2P" />
<Type class="CO2P" element="Co" mass="58.933" name="CO2P-CO2P" />
<Type class="NI2P" element="Ni" mass="58.693" name="NI2P-NI2P" />
<Type class="CU2P" element="Cu" mass="63.546" name="CU2P-CU2P" />
<Type class="PD2P" element="Pd" mass="106.42" name="PD2P-PD2P" />
<Type class="AG2P" element="Ag" mass="107.87" name="AG2P-AG2P" />
<Type class="SN2P" element="Sn" mass="118.71" name="SN2P-SN2P" />
<Type class="PT2P" element="Pt" mass="195.08" name="PT2P-PT2P" />
<Type class="HG2P" element="Hg" mass="200.59" name="HG2P-HG2P" />
<Type class="PB2P" element="Pb" mass="207.2" name="PB2P-PB2P" />
<Type class="SM2P" element="Sm" mass="150.36" name="SM2P-SM2P" />
<Type class="EU2P" element="Eu" mass="151.96" name="EU2P-EU2P" />
<Type class="YB2P" element="Yb" mass="173.05" name="YB2P-YB2P" />
<Type class="AL3P" element="Al" mass="26.982" name="AL3P-AL3P" />
<Type class="SC3P" element="Sc" mass="44.956" name="SC3P-SC3P" />
<Type class="Y3P" element="Y" mass="88.906" name="Y3P-Y3P" />
<Type class="LA3P" element="La" mass="138.91" name="LA3P-LA3P" />
<Type class="CE3P" element="Ce" mass="140.12" name="CE3P-CE3P" />
<Type class="PR3P" element="Pr" mass="140.91" name="PR3P-PR3P" />
<Type class="ND3P" element="Nd" mass="144.24" name="ND3P-ND3P" />
<Type class="PM3P" element="Pm" mass="144.91" name="PM3P-PM3P" />
<Type class="SM3P" element="Sm" mass="150.36" name="SM3P-SM3P" />
<Type class="EU3P" element="Eu" mass="151.96" name="EU3P-EU3P" />
<Type class="GD3P" element="Gd" mass="157.25" name="GD3P-GD3P" />
<Type class="TB3P" element="Tb" mass="158.93" name="TB3P-TB3P" />
<Type class="DY3P" element="Dy" mass="162.5" name="DY3P-DY3P" />
<Type class="HO3P" element="Ho" mass="164.93" name="HO3P-HO3P" />
<Type class="ER3P" element="Er" mass="167.28" name="ER3P-ER3P" />
<Type class="YB3P" element="Yb" mass="173.05" name="YB3P-YB3P" />
<Type class="LU3P" element="Lu" mass="174.97" name="LU3P-LU3P" />
<Type class="U3P" element="U" mass="238.03" name="U3P-U3P" />
<Type class="PU3P" element="Pu" mass="244.06" name="PU3P-PU3P" />
<Type class="TI3P" element="Ti" mass="47.867" name="TI3P-TI3P" />
<Type class="V3P" element="V" mass="50.942" name="V3P-V3P" />
<Type class="CR3P" element="Cr" mass="51.996" name="CR3P-CR3P" />
<Type class="MN3P" element="Mn" mass="54.938" name="MN3P-MN3P" />
<Type class="FE3P" element="Fe" mass="55.854" name="FE3P-FE3P" />
<Type class="CO3P" element="Co" mass="58.933" name="CO3P-CO3P" />
<Type class="GA3P" element="Ga" mass="69.723" name="GA3P-GA3P" />
<Type class="RH3P" element="Rh" mass="102.91" name="RH3P-RH3P" />
<Type class="IN3P" element="In" mass="114.82" name="IN3P-IN3P" />
<Type class="AU3P" element="Au" mass="196.97" name="AU3P-AU3P" />
<Type class="TL3P" element="Tl" mass="204.38" name="TL3P-TL3P" />
<Type class="BI3P" element="Bi" mass="208.98" name="BI3P-BI3P" />
</AtomTypes>
<Residues>
<Residue name="TP5E">
<Atom charge="0.0" name="OH2" type="TP5E-OH2" />
<Atom charge="0.241" name="H1" type="TP5E-H1" />
<Atom charge="0.241" name="H2" type="TP5E-H2" />
<Atom charge="-0.241" name="LP1" type="TP5E-LP1" />
<Atom charge="-0.241" name="LP2" type="TP5E-LP2" />
<Bond atomName1="OH2" atomName2="H1" />
<Bond atomName1="OH2" atomName2="H2" />
<VirtualSite atomName1="OH2" atomName2="H2" atomName3="H1" p1="-0.04041512765608711" p2="0" p3="0.057154330164408206" siteName="LP1" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OH2" atomName2="H2" atomName3="H1" p1="-0.04041512765608711" p2="0" p3="-0.057154330164408206" siteName="LP2" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1" />
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OH-O1" />
<Atom charge="0.32" name="H1" type="OH-H1" />
<Bond atomName1="O1" atomName2="H1" />
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT-LIT" />
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD-SOD" />
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG-MG" />
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT-POT" />
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL-CAL" />
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB-RUB" />
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES-CES" />
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR-BAR" />
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN2-ZN" />
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CD2-CD" />
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA-CLA" />
</Residue>
<Residue name="CU1P">
<Atom charge="1.0" name="CU1P" type="CU1P-CU1P" />
</Residue>
<Residue name="AG1P">
<Atom charge="1.0" name="AG1P" type="AG1P-AG1P" />
</Residue>
<Residue name="AU1P">
<Atom charge="1.0" name="AU1P" type="AU1P-AU1P" />
</Residue>
<Residue name="TI1P">
<Atom charge="1.0" name="TI1P" type="TI1P-TI1P" />
</Residue>
<Residue name="BE2P">
<Atom charge="2.0" name="BE2P" type="BE2P-BE2P" />
</Residue>
<Residue name="SR2P">
<Atom charge="2.0" name="SR2P" type="SR2P-SR2P" />
</Residue>
<Residue name="RA2P">
<Atom charge="2.0" name="RA2P" type="RA2P-RA2P" />
</Residue>
<Residue name="V2P">
<Atom charge="2.0" name="V2P" type="V2P-V2P" />
</Residue>
<Residue name="CR2P">
<Atom charge="2.0" name="CR2P" type="CR2P-CR2P" />
</Residue>
<Residue name="MN2P">
<Atom charge="2.0" name="MN2P" type="MN2P-MN2P" />
</Residue>
<Residue name="FE2P">
<Atom charge="2.0" name="FE2P" type="FE2P-FE2P" />
</Residue>
<Residue name="CO2P">
<Atom charge="2.0" name="CO2P" type="CO2P-CO2P" />
</Residue>
<Residue name="NI2P">
<Atom charge="2.0" name="NI2P" type="NI2P-NI2P" />
</Residue>
<Residue name="CU2P">
<Atom charge="2.0" name="CU2P" type="CU2P-CU2P" />
</Residue>
<Residue name="PD2P">
<Atom charge="2.0" name="PD2P" type="PD2P-PD2P" />
</Residue>
<Residue name="AG2P">
<Atom charge="2.0" name="AG2P" type="AG2P-AG2P" />
</Residue>
<Residue name="SN2P">
<Atom charge="2.0" name="SN2P" type="SN2P-SN2P" />
</Residue>
<Residue name="PT2P">
<Atom charge="2.0" name="PT2P" type="PT2P-PT2P" />
</Residue>
<Residue name="HG2P">
<Atom charge="2.0" name="HG2P" type="HG2P-HG2P" />
</Residue>
<Residue name="PB2P">
<Atom charge="2.0" name="PB2P" type="PB2P-PB2P" />
</Residue>
<Residue name="SM2P">
<Atom charge="2.0" name="SM2P" type="SM2P-SM2P" />
</Residue>
<Residue name="EU2P">
<Atom charge="2.0" name="EU2P" type="EU2P-EU2P" />
</Residue>
<Residue name="YB2P">
<Atom charge="2.0" name="YB2P" type="YB2P-YB2P" />
</Residue>
<Residue name="AL3P">
<Atom charge="3.0" name="AL3P" type="AL3P-AL3P" />
</Residue>
<Residue name="SC3P">
<Atom charge="3.0" name="SC3P" type="SC3P-SC3P" />
</Residue>
<Residue name="Y3P">
<Atom charge="3.0" name="Y3P" type="Y3P-Y3P" />
</Residue>
<Residue name="LA3P">
<Atom charge="3.0" name="LA3P" type="LA3P-LA3P" />
</Residue>
<Residue name="CE3P">
<Atom charge="3.0" name="CE3P" type="CE3P-CE3P" />
</Residue>
<Residue name="PR3P">
<Atom charge="3.0" name="PR3P" type="PR3P-PR3P" />
</Residue>
<Residue name="ND3P">
<Atom charge="3.0" name="ND3P" type="ND3P-ND3P" />
</Residue>
<Residue name="PM3P">
<Atom charge="3.0" name="PM3P" type="PM3P-PM3P" />
</Residue>
<Residue name="SM3P">
<Atom charge="3.0" name="SM3P" type="SM3P-SM3P" />
</Residue>
<Residue name="EU3P">
<Atom charge="3.0" name="EU3P" type="EU3P-EU3P" />
</Residue>
<Residue name="GD3P">
<Atom charge="3.0" name="GD3P" type="GD3P-GD3P" />
</Residue>
<Residue name="TB3P">
<Atom charge="3.0" name="TB3P" type="TB3P-TB3P" />
</Residue>
<Residue name="DY3P">
<Atom charge="3.0" name="DY3P" type="DY3P-DY3P" />
</Residue>
<Residue name="HO3P">
<Atom charge="3.0" name="HO3P" type="HO3P-HO3P" />
</Residue>
<Residue name="ER3P">
<Atom charge="3.0" name="ER3P" type="ER3P-ER3P" />
</Residue>
<Residue name="YB3P">
<Atom charge="3.0" name="YB3P" type="YB3P-YB3P" />
</Residue>
<Residue name="LU3P">
<Atom charge="3.0" name="LU3P" type="LU3P-LU3P" />
</Residue>
<Residue name="U3P">
<Atom charge="3.0" name="U3P" type="U3P-U3P" />
</Residue>
<Residue name="PU3P">
<Atom charge="3.0" name="PU3P" type="PU3P-PU3P" />
</Residue>
<Residue name="TI3P">
<Atom charge="3.0" name="TI3P" type="TI3P-TI3P" />
</Residue>
<Residue name="V3P">
<Atom charge="3.0" name="V3P" type="V3P-V3P" />
</Residue>
<Residue name="CR3P">
<Atom charge="3.0" name="CR3P" type="CR3P-CR3P" />
</Residue>
<Residue name="MN3P">
<Atom charge="3.0" name="MN3P" type="MN3P-MN3P" />
</Residue>
<Residue name="FE3P">
<Atom charge="3.0" name="FE3P" type="FE3P-FE3P" />
</Residue>
<Residue name="CO3P">
<Atom charge="3.0" name="CO3P" type="CO3P-CO3P" />
</Residue>
<Residue name="GA3P">
<Atom charge="3.0" name="GA3P" type="GA3P-GA3P" />
</Residue>
<Residue name="RH3P">
<Atom charge="3.0" name="RH3P" type="RH3P-RH3P" />
</Residue>
<Residue name="IN3P">
<Atom charge="3.0" name="IN3P" type="IN3P-IN3P" />
</Residue>
<Residue name="AU3P">
<Atom charge="3.0" name="AU3P" type="AU3P-AU3P" />
</Residue>
<Residue name="TL3P">
<Atom charge="3.0" name="TL3P" type="TL3P-TL3P" />
</Residue>
<Residue name="BI3P">
<Atom charge="3.0" name="BI3P" type="BI3P-BI3P" />
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="HT" class2="HT" k="0.0" length="0.15139000000000002" />
<Bond class1="HT" class2="OT" k="376559.99999999994" length="0.09572000000000001" />
<Bond class1="OX" class2="HX" k="456055.99999999994" length="0.097" />
<Bond class1="OT" class2="LP" k="0.0" length="0.06999999999999999" />
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" class1="HT" class2="OT" class3="HT" k="460.24" />
</HarmonicAngleForce>
<AmoebaUreyBradleyForce />
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge" />
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.0" sigma="1.0" />
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<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.35093300000000005" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.477963424" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.28419669108676826" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm36_2024/water.xml 0 → 100644
View file @ be646878
<ForceField>
<Info>
<DateGenerated>2025-02-27</DateGenerated>
<Source Source="toppar/toppar_water_ions.str" md5hash="1eba52cd9a244fa3df9a274a806d9128" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/toppar_water_ions.str</Source>
<Source Source="toppar/stream/misc/toppar_ions_won.str" md5hash="f523f7727e7dfa25468cc75f9b880c5b" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/stream/misc/toppar_ions_won.str</Source>
<Reference Reference="W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; &quot;Comparison of simple potential functions for simulating liquid water&quot;, J. Chem. Phys. 79 926-935 (1983)." forcefield="tip3p">W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; "Comparison of simple potential functions for simulating liquid water", J. Chem. Phys. 79 926-935 (1983).</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)" forcefield="ions">Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)</Reference>
<Reference Reference="Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012." forcefield="ions">Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.</Reference>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="TIP3-OH2" />
<Type class="HT" element="H" mass="1.008" name="TIP3-H1" />
<Type class="HT" element="H" mass="1.008" name="TIP3-H2" />
<Type class="OX" element="O" mass="15.9994" name="OH-O1" />
<Type class="HX" element="H" mass="1.008" name="OH-H1" />
<Type class="HPER" element="H" mass="1.008" name="H2O2-HP1" />
<Type class="OPER" element="O" mass="15.999" name="H2O2-OP1" />
<Type class="OPER" element="O" mass="15.999" name="H2O2-OP2" />
<Type class="HPER" element="H" mass="1.008" name="H2O2-HP2" />
<Type class="LIT" element="Li" mass="6.941" name="LIT-LIT" />
<Type class="SOD" element="Na" mass="22.98977" name="SOD-SOD" />
<Type class="MG" element="Mg" mass="24.305" name="MG-MG" />
<Type class="POT" element="K" mass="39.0983" name="POT-POT" />
<Type class="CAL" element="Ca" mass="40.08" name="CAL-CAL" />
<Type class="RUB" element="Rb" mass="85.4678" name="RUB-RUB" />
<Type class="CES" element="Cs" mass="132.90545" name="CES-CES" />
<Type class="BAR" element="Ba" mass="137.327" name="BAR-BAR" />
<Type class="ZN" element="Zn" mass="65.37" name="ZN2-ZN" />
<Type class="CAD" element="Cd" mass="112.411" name="CD2-CD" />
<Type class="CLA" element="Cl" mass="35.45" name="CLA-CLA" />
<Type class="CU1P" element="Cu" mass="63.546" name="CU1P-CU1P" />
<Type class="AG1P" element="Ag" mass="107.87" name="AG1P-AG1P" />
<Type class="AU1P" element="Au" mass="196.97" name="AU1P-AU1P" />
<Type class="TI1P" element="Ti" mass="47.867" name="TI1P-TI1P" />
<Type class="BE2P" element="Be" mass="9.0122" name="BE2P-BE2P" />
<Type class="SR2P" element="Sr" mass="87.62" name="SR2P-SR2P" />
<Type class="RA2P" element="Ra" mass="226.03" name="RA2P-RA2P" />
<Type class="V2P" element="V" mass="50.942" name="V2P-V2P" />
<Type class="CR2P" element="Cr" mass="51.996" name="CR2P-CR2P" />
<Type class="MN2P" element="Mn" mass="54.938" name="MN2P-MN2P" />
<Type class="FE2P" element="Fe" mass="55.854" name="FE2P-FE2P" />
<Type class="CO2P" element="Co" mass="58.933" name="CO2P-CO2P" />
<Type class="NI2P" element="Ni" mass="58.693" name="NI2P-NI2P" />
<Type class="CU2P" element="Cu" mass="63.546" name="CU2P-CU2P" />
<Type class="PD2P" element="Pd" mass="106.42" name="PD2P-PD2P" />
<Type class="AG2P" element="Ag" mass="107.87" name="AG2P-AG2P" />
<Type class="SN2P" element="Sn" mass="118.71" name="SN2P-SN2P" />
<Type class="PT2P" element="Pt" mass="195.08" name="PT2P-PT2P" />
<Type class="HG2P" element="Hg" mass="200.59" name="HG2P-HG2P" />
<Type class="PB2P" element="Pb" mass="207.2" name="PB2P-PB2P" />
<Type class="SM2P" element="Sm" mass="150.36" name="SM2P-SM2P" />
<Type class="EU2P" element="Eu" mass="151.96" name="EU2P-EU2P" />
<Type class="YB2P" element="Yb" mass="173.05" name="YB2P-YB2P" />
<Type class="AL3P" element="Al" mass="26.982" name="AL3P-AL3P" />
<Type class="SC3P" element="Sc" mass="44.956" name="SC3P-SC3P" />
<Type class="Y3P" element="Y" mass="88.906" name="Y3P-Y3P" />
<Type class="LA3P" element="La" mass="138.91" name="LA3P-LA3P" />
<Type class="CE3P" element="Ce" mass="140.12" name="CE3P-CE3P" />
<Type class="PR3P" element="Pr" mass="140.91" name="PR3P-PR3P" />
<Type class="ND3P" element="Nd" mass="144.24" name="ND3P-ND3P" />
<Type class="PM3P" element="Pm" mass="144.91" name="PM3P-PM3P" />
<Type class="SM3P" element="Sm" mass="150.36" name="SM3P-SM3P" />
<Type class="EU3P" element="Eu" mass="151.96" name="EU3P-EU3P" />
<Type class="GD3P" element="Gd" mass="157.25" name="GD3P-GD3P" />
<Type class="TB3P" element="Tb" mass="158.93" name="TB3P-TB3P" />
<Type class="DY3P" element="Dy" mass="162.5" name="DY3P-DY3P" />
<Type class="HO3P" element="Ho" mass="164.93" name="HO3P-HO3P" />
<Type class="ER3P" element="Er" mass="167.28" name="ER3P-ER3P" />
<Type class="YB3P" element="Yb" mass="173.05" name="YB3P-YB3P" />
<Type class="LU3P" element="Lu" mass="174.97" name="LU3P-LU3P" />
<Type class="U3P" element="U" mass="238.03" name="U3P-U3P" />
<Type class="PU3P" element="Pu" mass="244.06" name="PU3P-PU3P" />
<Type class="TI3P" element="Ti" mass="47.867" name="TI3P-TI3P" />
<Type class="V3P" element="V" mass="50.942" name="V3P-V3P" />
<Type class="CR3P" element="Cr" mass="51.996" name="CR3P-CR3P" />
<Type class="MN3P" element="Mn" mass="54.938" name="MN3P-MN3P" />
<Type class="FE3P" element="Fe" mass="55.854" name="FE3P-FE3P" />
<Type class="CO3P" element="Co" mass="58.933" name="CO3P-CO3P" />
<Type class="GA3P" element="Ga" mass="69.723" name="GA3P-GA3P" />
<Type class="RH3P" element="Rh" mass="102.91" name="RH3P-RH3P" />
<Type class="IN3P" element="In" mass="114.82" name="IN3P-IN3P" />
<Type class="AU3P" element="Au" mass="196.97" name="AU3P-AU3P" />
<Type class="TL3P" element="Tl" mass="204.38" name="TL3P-TL3P" />
<Type class="BI3P" element="Bi" mass="208.98" name="BI3P-BI3P" />
</AtomTypes>
<Residues>
<Residue name="TIP3">
<Atom charge="-0.834" name="OH2" type="TIP3-OH2" />
<Atom charge="0.417" name="H1" type="TIP3-H1" />
<Atom charge="0.417" name="H2" type="TIP3-H2" />
<Bond atomName1="OH2" atomName2="H1" />
<Bond atomName1="OH2" atomName2="H2" />
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OH-O1" />
<Atom charge="0.32" name="H1" type="OH-H1" />
<Bond atomName1="O1" atomName2="H1" />
</Residue>
<Residue name="H2O2">
<Atom charge="0.41" name="HP1" type="H2O2-HP1" />
<Atom charge="-0.41" name="OP1" type="H2O2-OP1" />
<Atom charge="-0.41" name="OP2" type="H2O2-OP2" />
<Atom charge="0.41" name="HP2" type="H2O2-HP2" />
<Bond atomName1="HP1" atomName2="OP1" />
<Bond atomName1="OP1" atomName2="OP2" />
<Bond atomName1="OP2" atomName2="HP2" />
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT-LIT" />
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD-SOD" />
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG-MG" />
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT-POT" />
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL-CAL" />
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB-RUB" />
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES-CES" />
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR-BAR" />
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN2-ZN" />
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CD2-CD" />
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA-CLA" />
</Residue>
<Residue name="CU1P">
<Atom charge="1.0" name="CU1P" type="CU1P-CU1P" />
</Residue>
<Residue name="AG1P">
<Atom charge="1.0" name="AG1P" type="AG1P-AG1P" />
</Residue>
<Residue name="AU1P">
<Atom charge="1.0" name="AU1P" type="AU1P-AU1P" />
</Residue>
<Residue name="TI1P">
<Atom charge="1.0" name="TI1P" type="TI1P-TI1P" />
</Residue>
<Residue name="BE2P">
<Atom charge="2.0" name="BE2P" type="BE2P-BE2P" />
</Residue>
<Residue name="SR2P">
<Atom charge="2.0" name="SR2P" type="SR2P-SR2P" />
</Residue>
<Residue name="RA2P">
<Atom charge="2.0" name="RA2P" type="RA2P-RA2P" />
</Residue>
<Residue name="V2P">
<Atom charge="2.0" name="V2P" type="V2P-V2P" />
</Residue>
<Residue name="CR2P">
<Atom charge="2.0" name="CR2P" type="CR2P-CR2P" />
</Residue>
<Residue name="MN2P">
<Atom charge="2.0" name="MN2P" type="MN2P-MN2P" />
</Residue>
<Residue name="FE2P">
<Atom charge="2.0" name="FE2P" type="FE2P-FE2P" />
</Residue>
<Residue name="CO2P">
<Atom charge="2.0" name="CO2P" type="CO2P-CO2P" />
</Residue>
<Residue name="NI2P">
<Atom charge="2.0" name="NI2P" type="NI2P-NI2P" />
</Residue>
<Residue name="CU2P">
<Atom charge="2.0" name="CU2P" type="CU2P-CU2P" />
</Residue>
<Residue name="PD2P">
<Atom charge="2.0" name="PD2P" type="PD2P-PD2P" />
</Residue>
<Residue name="AG2P">
<Atom charge="2.0" name="AG2P" type="AG2P-AG2P" />
</Residue>
<Residue name="SN2P">
<Atom charge="2.0" name="SN2P" type="SN2P-SN2P" />
</Residue>
<Residue name="PT2P">
<Atom charge="2.0" name="PT2P" type="PT2P-PT2P" />
</Residue>
<Residue name="HG2P">
<Atom charge="2.0" name="HG2P" type="HG2P-HG2P" />
</Residue>
<Residue name="PB2P">
<Atom charge="2.0" name="PB2P" type="PB2P-PB2P" />
</Residue>
<Residue name="SM2P">
<Atom charge="2.0" name="SM2P" type="SM2P-SM2P" />
</Residue>
<Residue name="EU2P">
<Atom charge="2.0" name="EU2P" type="EU2P-EU2P" />
</Residue>
<Residue name="YB2P">
<Atom charge="2.0" name="YB2P" type="YB2P-YB2P" />
</Residue>
<Residue name="AL3P">
<Atom charge="3.0" name="AL3P" type="AL3P-AL3P" />
</Residue>
<Residue name="SC3P">
<Atom charge="3.0" name="SC3P" type="SC3P-SC3P" />
</Residue>
<Residue name="Y3P">
<Atom charge="3.0" name="Y3P" type="Y3P-Y3P" />
</Residue>
<Residue name="LA3P">
<Atom charge="3.0" name="LA3P" type="LA3P-LA3P" />
</Residue>
<Residue name="CE3P">
<Atom charge="3.0" name="CE3P" type="CE3P-CE3P" />
</Residue>
<Residue name="PR3P">
<Atom charge="3.0" name="PR3P" type="PR3P-PR3P" />
</Residue>
<Residue name="ND3P">
<Atom charge="3.0" name="ND3P" type="ND3P-ND3P" />
</Residue>
<Residue name="PM3P">
<Atom charge="3.0" name="PM3P" type="PM3P-PM3P" />
</Residue>
<Residue name="SM3P">
<Atom charge="3.0" name="SM3P" type="SM3P-SM3P" />
</Residue>
<Residue name="EU3P">
<Atom charge="3.0" name="EU3P" type="EU3P-EU3P" />
</Residue>
<Residue name="GD3P">
<Atom charge="3.0" name="GD3P" type="GD3P-GD3P" />
</Residue>
<Residue name="TB3P">
<Atom charge="3.0" name="TB3P" type="TB3P-TB3P" />
</Residue>
<Residue name="DY3P">
<Atom charge="3.0" name="DY3P" type="DY3P-DY3P" />
</Residue>
<Residue name="HO3P">
<Atom charge="3.0" name="HO3P" type="HO3P-HO3P" />
</Residue>
<Residue name="ER3P">
<Atom charge="3.0" name="ER3P" type="ER3P-ER3P" />
</Residue>
<Residue name="YB3P">
<Atom charge="3.0" name="YB3P" type="YB3P-YB3P" />
</Residue>
<Residue name="LU3P">
<Atom charge="3.0" name="LU3P" type="LU3P-LU3P" />
</Residue>
<Residue name="U3P">
<Atom charge="3.0" name="U3P" type="U3P-U3P" />
</Residue>
<Residue name="PU3P">
<Atom charge="3.0" name="PU3P" type="PU3P-PU3P" />
</Residue>
<Residue name="TI3P">
<Atom charge="3.0" name="TI3P" type="TI3P-TI3P" />
</Residue>
<Residue name="V3P">
<Atom charge="3.0" name="V3P" type="V3P-V3P" />
</Residue>
<Residue name="CR3P">
<Atom charge="3.0" name="CR3P" type="CR3P-CR3P" />
</Residue>
<Residue name="MN3P">
<Atom charge="3.0" name="MN3P" type="MN3P-MN3P" />
</Residue>
<Residue name="FE3P">
<Atom charge="3.0" name="FE3P" type="FE3P-FE3P" />
</Residue>
<Residue name="CO3P">
<Atom charge="3.0" name="CO3P" type="CO3P-CO3P" />
</Residue>
<Residue name="GA3P">
<Atom charge="3.0" name="GA3P" type="GA3P-GA3P" />
</Residue>
<Residue name="RH3P">
<Atom charge="3.0" name="RH3P" type="RH3P-RH3P" />
</Residue>
<Residue name="IN3P">
<Atom charge="3.0" name="IN3P" type="IN3P-IN3P" />
</Residue>
<Residue name="AU3P">
<Atom charge="3.0" name="AU3P" type="AU3P-AU3P" />
</Residue>
<Residue name="TL3P">
<Atom charge="3.0" name="TL3P" type="TL3P-TL3P" />
</Residue>
<Residue name="BI3P">
<Atom charge="3.0" name="BI3P" type="BI3P-BI3P" />
</Residue>
</Residues>
<HarmonicBondForce>
<Bond class1="HT" class2="HT" k="0.0" length="0.15139000000000002" />
<Bond class1="HT" class2="OT" k="376559.99999999994" length="0.09572000000000001" />
<Bond class1="OX" class2="HX" k="456055.99999999994" length="0.097" />
<Bond class1="HPER" class2="OPER" k="435972.79999999993" length="0.0963" />
<Bond class1="OPER" class2="OPER" k="238906.39999999997" length="0.1442" />
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" class1="HT" class2="OT" class3="HT" k="460.24" />
<Angle angle="1.7439329885927342" class1="HPER" class2="OPER" class3="OPER" k="505.4272" />
</HarmonicAngleForce>
<AmoebaUreyBradleyForce />
<PeriodicTorsionForce>
<Proper class1="HPER" class2="OPER" class3="OPER" class4="HPER" k1="8.45168" periodicity1="2" phase1="0.0" />
</PeriodicTorsionForce>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge" />
<Atom class="HT" epsilon="0.0" sigma="1.0" />
<Atom class="HX" epsilon="0.0" sigma="1.0" />
<Atom class="OT" epsilon="0.0" sigma="1.0" />
<Atom class="OX" epsilon="0.0" sigma="1.0" />
<Atom class="HPER" epsilon="0.0" sigma="1.0" />
<Atom class="OPER" epsilon="0.0" sigma="1.0" />
<Atom class="LIT" epsilon="0.0" sigma="1.0" />
<Atom class="SOD" epsilon="0.0" sigma="1.0" />
<Atom class="MG" epsilon="0.0" sigma="1.0" />
<Atom class="POT" epsilon="0.0" sigma="1.0" />
<Atom class="CAL" epsilon="0.0" sigma="1.0" />
<Atom class="RUB" epsilon="0.0" sigma="1.0" />
<Atom class="CES" epsilon="0.0" sigma="1.0" />
<Atom class="BAR" epsilon="0.0" sigma="1.0" />
<Atom class="ZN" epsilon="0.0" sigma="1.0" />
<Atom class="CAD" epsilon="0.0" sigma="1.0" />
<Atom class="CLA" epsilon="0.0" sigma="1.0" />
<Atom class="CU1P" epsilon="0.0" sigma="1.0" />
<Atom class="AG1P" epsilon="0.0" sigma="1.0" />
<Atom class="AU1P" epsilon="0.0" sigma="1.0" />
<Atom class="TI1P" epsilon="0.0" sigma="1.0" />
<Atom class="BE2P" epsilon="0.0" sigma="1.0" />
<Atom class="SR2P" epsilon="0.0" sigma="1.0" />
<Atom class="RA2P" epsilon="0.0" sigma="1.0" />
<Atom class="V2P" epsilon="0.0" sigma="1.0" />
<Atom class="CR2P" epsilon="0.0" sigma="1.0" />
<Atom class="MN2P" epsilon="0.0" sigma="1.0" />
<Atom class="FE2P" epsilon="0.0" sigma="1.0" />
<Atom class="CO2P" epsilon="0.0" sigma="1.0" />
<Atom class="NI2P" epsilon="0.0" sigma="1.0" />
<Atom class="CU2P" epsilon="0.0" sigma="1.0" />
<Atom class="PD2P" epsilon="0.0" sigma="1.0" />
<Atom class="AG2P" epsilon="0.0" sigma="1.0" />
<Atom class="SN2P" epsilon="0.0" sigma="1.0" />
<Atom class="PT2P" epsilon="0.0" sigma="1.0" />
<Atom class="HG2P" epsilon="0.0" sigma="1.0" />
<Atom class="PB2P" epsilon="0.0" sigma="1.0" />
<Atom class="SM2P" epsilon="0.0" sigma="1.0" />
<Atom class="EU2P" epsilon="0.0" sigma="1.0" />
<Atom class="YB2P" epsilon="0.0" sigma="1.0" />
<Atom class="AL3P" epsilon="0.0" sigma="1.0" />
<Atom class="SC3P" epsilon="0.0" sigma="1.0" />
<Atom class="Y3P" epsilon="0.0" sigma="1.0" />
<Atom class="LA3P" epsilon="0.0" sigma="1.0" />
<Atom class="CE3P" epsilon="0.0" sigma="1.0" />
<Atom class="PR3P" epsilon="0.0" sigma="1.0" />
<Atom class="ND3P" epsilon="0.0" sigma="1.0" />
<Atom class="PM3P" epsilon="0.0" sigma="1.0" />
<Atom class="SM3P" epsilon="0.0" sigma="1.0" />
<Atom class="EU3P" epsilon="0.0" sigma="1.0" />
<Atom class="GD3P" epsilon="0.0" sigma="1.0" />
<Atom class="TB3P" epsilon="0.0" sigma="1.0" />
<Atom class="DY3P" epsilon="0.0" sigma="1.0" />
<Atom class="HO3P" epsilon="0.0" sigma="1.0" />
<Atom class="ER3P" epsilon="0.0" sigma="1.0" />
<Atom class="TM3P" epsilon="0.0" sigma="1.0" />
<Atom class="YB3P" epsilon="0.0" sigma="1.0" />
<Atom class="LU3P" epsilon="0.0" sigma="1.0" />
<Atom class="U3P" epsilon="0.0" sigma="1.0" />
<Atom class="PU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TI3P" epsilon="0.0" sigma="1.0" />
<Atom class="V3P" epsilon="0.0" sigma="1.0" />
<Atom class="CR3P" epsilon="0.0" sigma="1.0" />
<Atom class="MN3P" epsilon="0.0" sigma="1.0" />
<Atom class="FE3P" epsilon="0.0" sigma="1.0" />
<Atom class="CO3P" epsilon="0.0" sigma="1.0" />
<Atom class="GA3P" epsilon="0.0" sigma="1.0" />
<Atom class="RH3P" epsilon="0.0" sigma="1.0" />
<Atom class="IN3P" epsilon="0.0" sigma="1.0" />
<Atom class="AU3P" epsilon="0.0" sigma="1.0" />
<Atom class="TL3P" epsilon="0.0" sigma="1.0" />
<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom class="HT" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="HX" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="OT" epsilon="0.6363864000000001" sigma="0.3150574226831496" />
<Atom class="OX" epsilon="0.50208" sigma="0.30290556416771536" />
<Atom class="HPER" epsilon="0.192464" sigma="0.04000135244450124" />
<Atom class="OPER" epsilon="0.85286656" sigma="0.29831387217442007" />
<Atom class="LIT" epsilon="0.00974872" sigma="0.23118821735741807" />
<Atom class="SOD" epsilon="0.1962296" sigma="0.2513670733232967" />
<Atom class="MG" epsilon="0.06276" sigma="0.2111429961992604" />
<Atom class="POT" epsilon="0.364008" sigma="0.3142645228240047" />
<Atom class="CAL" epsilon="0.50208" sigma="0.24357170953956878" />
<Atom class="RUB" epsilon="0.6276" sigma="0.3385415128933289" />
<Atom class="CES" epsilon="0.79496" sigma="0.37417746161894255" />
<Atom class="BAR" epsilon="0.6276" sigma="0.33675971545704825" />
<Atom class="ZN" epsilon="1.046" sigma="0.194215920554594" />
<Atom class="CAD" epsilon="0.50208" sigma="0.2417899121032881" />
<Atom class="CLA" epsilon="0.6276" sigma="0.4044680180357141" />
<Atom class="CU1P" epsilon="0.7748768" sigma="0.1535909390073945" />
<Atom class="AG1P" epsilon="1.2008079999999999" sigma="0.2163636626875628" />
<Atom class="AU1P" epsilon="1.4907592" sigma="0.11250269012676205" />
<Atom class="TI1P" epsilon="1.7016328" sigma="0.34401163102271065" />
<Atom class="BE2P" epsilon="0.4250944" sigma="0.007127189745122714" />
<Atom class="SR2P" epsilon="0.9572992" sigma="0.3306837861993312" />
<Atom class="RA2P" epsilon="1.2631496" sigma="0.37237784620829906" />
<Atom class="V2P" epsilon="0.6732056" sigma="0.1966569830422985" />
<Atom class="CR2P" epsilon="0.6974728" sigma="0.18872798445084948" />
<Atom class="MN2P" epsilon="0.7050040000000001" sigma="0.2144749574051053" />
<Atom class="FE2P" epsilon="0.667348" sigma="0.1924519410926761" />
<Atom class="CO2P" epsilon="0.6439176000000001" sigma="0.16527953018939576" />
<Atom class="NI2P" epsilon="0.5999856" sigma="0.13903365395298137" />
<Atom class="CU2P" epsilon="0.629692" sigma="0.129198132104712" />
<Atom class="PD2P" epsilon="0.7288528" sigma="0.16519044031758173" />
<Atom class="AG2P" epsilon="0.7752952" sigma="0.1869105510658432" />
<Atom class="SN2P" epsilon="0.7861736" sigma="0.29542201493533654" />
<Atom class="PT2P" epsilon="0.6824104" sigma="0.1420270736459329" />
<Atom class="HG2P" epsilon="0.8593936" sigma="0.2105728210196506" />
<Atom class="PB2P" epsilon="1.0016496000000001" sigma="0.3132399892981433" />
<Atom class="SM2P" epsilon="1.0242432" sigma="0.330790694045508" />
<Atom class="EU2P" epsilon="0.9907712000000001" sigma="0.3279220001730961" />
<Atom class="YB2P" epsilon="0.8593936" sigma="0.28669120749756116" />
<Atom class="AL3P" epsilon="0.44601440000000003" sigma="0.039377723341803" />
<Atom class="SC3P" epsilon="0.5899439999999999" sigma="0.19544536078562763" />
<Atom class="Y3P" epsilon="0.6928704" sigma="0.25183924964391113" />
<Atom class="LA3P" epsilon="0.7932864" sigma="0.3158592315294759" />
<Atom class="CE3P" epsilon="0.7702744000000001" sigma="0.30495463121943817" />
<Atom class="PR3P" epsilon="0.7627432" sigma="0.2956180126533274" />
<Atom class="ND3P" epsilon="0.7497728" sigma="0.2886333667031071" />
<Atom class="PM3P" epsilon="0.74266" sigma="0.29527947114043407" />
<Atom class="SM3P" epsilon="0.7351288" sigma="0.2791542043420939" />
<Atom class="EU3P" epsilon="0.728016" sigma="0.2713677495455473" />
<Atom class="GD3P" epsilon="0.7209032000000001" sigma="0.2681605141602421" />
<Atom class="TB3P" epsilon="0.7083512000000001" sigma="0.2628151218514001" />
<Atom class="DY3P" epsilon="0.6999832" sigma="0.2573628216963812" />
<Atom class="HO3P" epsilon="0.6928704" sigma="0.247794569463554" />
<Atom class="ER3P" epsilon="0.6845024" sigma="0.24362516346265717" />
<Atom class="TM3P" epsilon="0.6778080000000001" sigma="0.24029320225681233" />
<Atom class="YB3P" epsilon="0.6711136" sigma="0.23077840394707347" />
<Atom class="LU3P" epsilon="0.6644192" sigma="0.2407564695902453" />
<Atom class="U3P" epsilon="0.7932864" sigma="0.3031193798600691" />
<Atom class="PU3P" epsilon="0.7702744000000001" sigma="0.29750671793578487" />
<Atom class="TI3P" epsilon="0.537644" sigma="0.14769318949330543" />
<Atom class="V3P" epsilon="0.5171424" sigma="0.10943799853635927" />
<Atom class="CR3P" epsilon="0.5045904" sigma="0.15022334185282402" />
<Atom class="MN3P" epsilon="0.5238368" sigma="0.06849229345062928" />
<Atom class="FE3P" epsilon="0.5238368" sigma="0.10090318881657484" />
<Atom class="CO3P" epsilon="0.4983144" sigma="0.04598819183040431" />
<Atom class="GA3P" epsilon="0.5045904" sigma="0.04042898382920859" />
<Atom class="RH3P" epsilon="0.537644" sigma="0.0821943157356277" />
<Atom class="IN3P" epsilon="0.6163031999999999" sigma="0.15435711190499518" />
<Atom class="AU3P" epsilon="0.5564720000000001" sigma="0.065106878321696" />
<Atom class="TL3P" epsilon="0.6815736" sigma="0.15489165113587938" />
<Atom class="BI3P" epsilon="0.7740400000000001" sigma="0.24378552523192246" />
<NBFixPair class1="OC" class2="SOD" epsilon="0.31388368000000005" sigma="0.2877602859593296" />
<NBFixPair class1="OS" class2="SOD" epsilon="0.31388368000000005" sigma="0.2788512987779262" />
<NBFixPair class1="LIT" class2="ON3" epsilon="0.0698728" sigma="0.28308306768909286" />
<NBFixPair class1="OCL" class2="SOD" epsilon="0.31388368000000005" sigma="0.2877602859593296" />
<NBFixPair class1="OBL" class2="SOD" epsilon="0.31388368000000005" sigma="0.2788512987779262" />
<NBFixPair class1="O2L" class2="SOD" epsilon="0.31388368000000005" sigma="0.28152399493234725" />
<NBFixPair class1="OC2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.2877602859593296" />
<NBFixPair class1="OC2DP" class2="SOD" epsilon="0.31388368000000005" sigma="0.28152399493234725" />
<NBFixPair class1="OG2D2" class2="SOD" epsilon="0.31388368000000005" sigma="0.2877602859593296" />
<NBFixPair class1="OG2P1" class2="SOD" epsilon="0.31388368000000005" sigma="0.28152399493234725" />
<NBFixPair class1="CLA" class2="LIT" epsilon="0.07824080000000001" sigma="0.3285189023142501" />
<NBFixPair class1="CLA" class2="SOD" epsilon="0.3510376" sigma="0.3323943117381606" />
<NBFixPair class1="CLA" class2="POT" epsilon="0.4778128" sigma="0.3635757668730725" />
<NBFixPair class1="OC" class2="POT" epsilon="0.4276048" sigma="0.3139527082726556" />
<NBFixPair class1="OCL" class2="POT" epsilon="0.4276048" sigma="0.3139527082726556" />
<NBFixPair class1="OC2D2" class2="POT" epsilon="0.4276048" sigma="0.3139527082726556" />
<NBFixPair class1="OG2D2" class2="POT" epsilon="0.4276048" sigma="0.3139527082726556" />
<NBFixPair class1="CAL" class2="CLA" epsilon="0.561342176" sigma="0.3320379522509045" />
<NBFixPair class1="CAL" class2="O2L" epsilon="0.50208" sigma="0.2900766226264945" />
<NBFixPair class1="CAL" class2="OC2DP" epsilon="0.50208" sigma="0.2900766226264945" />
<NBFixPair class1="CAL" class2="OG2P1" epsilon="0.50208" sigma="0.2900766226264945" />
<NBFixPair class1="CAL" class2="OCL" epsilon="0.50208" sigma="0.28793846570295767" />
<NBFixPair class1="CAL" class2="OC" epsilon="0.50208" sigma="0.28793846570295767" />
<NBFixPair class1="CAL" class2="OC2D2" epsilon="0.50208" sigma="0.28793846570295767" />
<NBFixPair class1="CAL" class2="OG2D2" epsilon="0.50208" sigma="0.28793846570295767" />
</LennardJonesForce>
<InitializationScript>
EXPECTED_VERSION = "charmm36_2024"
if hasattr(self, "_charmm_ff_version"):
if self._charmm_ff_version != EXPECTED_VERSION:
raise RuntimeError(f"CHARMM force field versions ({self._charmm_ff_version} and {EXPECTED_VERSION}) incompatible")
else:
self._charmm_ff_version = EXPECTED_VERSION
</InitializationScript>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/charmm_polar_2023.xml
View file @ be646878
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2025-02-27</DateGenerated> <DateGenerated>2025-06-23</DateGenerated>
<Source Source="toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str" md5hash="f3c4caab3ff08e7b822f7b944db3f197" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str</Source> <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str" md5hash="f3c4caab3ff08e7b822f7b944db3f197" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_main_protein_2023a.str</Source>
<Source Source="toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str" md5hash="192af93e684f3891df130182b8302c58" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str</Source> <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str" md5hash="192af93e684f3891df130182b8302c58" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_d_aminoacids_2023a.str</Source>
<Source Source="toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str" md5hash="6d8a686b8b5ecf19de7e598d928a7c1a" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str</Source> <Source Source="toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str" md5hash="6d8a686b8b5ecf19de7e598d928a7c1a" sourcePackage="drude" sourcePackageVersion="drude_toppar_2023.tgz">toppar/drude/drude_toppar_2023/toppar_drude_carbohydrate_2023a.str</Source>
...@@ -9684,15 +9684,6 @@ ...@@ -9684,15 +9684,6 @@
<Type class="DRUD" mass="0.0" name="Drude-GNTE-O" /> <Type class="DRUD" mass="0.0" name="Drude-GNTE-O" />
<Type class="LPDO1" mass="0.0" name="GNTE-LPOA" /> <Type class="LPDO1" mass="0.0" name="GNTE-LPOA" />
<Type class="LPDO1" mass="0.0" name="GNTE-LPOB" /> <Type class="LPDO1" mass="0.0" name="GNTE-LPOB" />
<Type class="ND3P3A" element="N" mass="14.007" name="GNTS-N" />
<Type class="DRUD" mass="0.0" name="Drude-GNTS-N" />
<Type class="HDP1B" element="H" mass="1.008" name="GNTS-HT1" />
<Type class="HDP1B" element="H" mass="1.008" name="GNTS-HT2" />
<Type class="HDP1B" element="H" mass="1.008" name="GNTS-HT3" />
<Type class="CD32C" element="C" mass="12.011" name="GNTS-CA" />
<Type class="DRUD" mass="0.0" name="Drude-GNTS-CA" />
<Type class="HDA2C" element="H" mass="1.008" name="GNTS-HA1" />
<Type class="HDA2C" element="H" mass="1.008" name="GNTS-HA2" />
<Type class="ND3P2A" element="N" mass="14.007" name="PROP-N" /> <Type class="ND3P2A" element="N" mass="14.007" name="PROP-N" />
<Type class="DRUD" mass="0.0" name="Drude-PROP-N" /> <Type class="DRUD" mass="0.0" name="Drude-PROP-N" />
<Type class="HDP1B" element="H" mass="1.008" name="PROP-HT1" /> <Type class="HDP1B" element="H" mass="1.008" name="PROP-HT1" />
...@@ -9855,17 +9846,6 @@ ...@@ -9855,17 +9846,6 @@
<Type class="LPD" mass="0.0" name="CNEG-LPT2" /> <Type class="LPD" mass="0.0" name="CNEG-LPT2" />
<Type class="LPD" mass="0.0" name="CNEG-LPT3" /> <Type class="LPD" mass="0.0" name="CNEG-LPT3" />
<Type class="LPD" mass="0.0" name="CNEG-LPT4" /> <Type class="LPD" mass="0.0" name="CNEG-LPT4" />
<Type class="CD2O3A" element="C" mass="12.011" name="CNES-C" />
<Type class="DRUD" mass="0.0" name="Drude-CNES-C" />
<Type class="OD2C3A" element="O" mass="15.9994" name="CNES-OT1" />
<Type class="DRUD" mass="0.0" name="Drude-CNES-OT1" />
<Type class="OD31F" element="O" mass="15.9994" name="CNES-OT2" />
<Type class="DRUD" mass="0.0" name="Drude-CNES-OT2" />
<Type class="HDP1A" element="H" mass="1.008" name="CNES-HT" />
<Type class="LPD" mass="0.0" name="CNES-LPT1" />
<Type class="LPD" mass="0.0" name="CNES-LPT2" />
<Type class="LPD" mass="0.0" name="CNES-LPT3" />
<Type class="LPD" mass="0.0" name="CNES-LPT4" />
<Type class="ND2A2" element="N" mass="14.007" name="CT1-N" /> <Type class="ND2A2" element="N" mass="14.007" name="CT1-N" />
<Type class="DRUD" mass="0.0" name="Drude-CT1-N" /> <Type class="DRUD" mass="0.0" name="Drude-CT1-N" />
<Type class="HDP1A" element="H" mass="1.008" name="CT1-HN" /> <Type class="HDP1A" element="H" mass="1.008" name="CT1-HN" />
...@@ -9942,16 +9922,6 @@ ...@@ -9942,16 +9922,6 @@
<Type class="HDP1A" element="H" mass="1.008" name="CT2G-HTC2" /> <Type class="HDP1A" element="H" mass="1.008" name="CT2G-HTC2" />
<Type class="LPDO1" mass="0.0" name="CT2G-LPOA" /> <Type class="LPDO1" mass="0.0" name="CT2G-LPOA" />
<Type class="LPDO1" mass="0.0" name="CT2G-LPOB" /> <Type class="LPDO1" mass="0.0" name="CT2G-LPOB" />
<Type class="CD2O1A" element="C" mass="12.011" name="CT2S-C" />
<Type class="DRUD" mass="0.0" name="Drude-CT2S-C" />
<Type class="OD2C1A" element="O" mass="15.9994" name="CT2S-O" />
<Type class="DRUD" mass="0.0" name="Drude-CT2S-O" />
<Type class="ND2A1" element="N" mass="14.007" name="CT2S-NT" />
<Type class="DRUD" mass="0.0" name="Drude-CT2S-NT" />
<Type class="HDP1A" element="H" mass="1.008" name="CT2S-HTC1" />
<Type class="HDP1A" element="H" mass="1.008" name="CT2S-HTC2" />
<Type class="LPDO1" mass="0.0" name="CT2S-LPOA" />
<Type class="LPDO1" mass="0.0" name="CT2S-LPOB" />
<Type class="ND2A2" element="N" mass="14.007" name="CT3-NT" /> <Type class="ND2A2" element="N" mass="14.007" name="CT3-NT" />
<Type class="DRUD" mass="0.0" name="Drude-CT3-NT" /> <Type class="DRUD" mass="0.0" name="Drude-CT3-NT" />
<Type class="HDP1A" element="H" mass="1.008" name="CT3-HNT" /> <Type class="HDP1A" element="H" mass="1.008" name="CT3-HNT" />
...@@ -10059,6 +10029,15 @@ ...@@ -10059,6 +10029,15 @@
<Type class="CD31DC" element="C" mass="12.011" name="DNTES-CA" /> <Type class="CD31DC" element="C" mass="12.011" name="DNTES-CA" />
<Type class="DRUD" mass="0.0" name="Drude-DNTES-CA" /> <Type class="DRUD" mass="0.0" name="Drude-DNTES-CA" />
<Type class="HDA1C" element="H" mass="1.008" name="DNTES-HA" /> <Type class="HDA1C" element="H" mass="1.008" name="DNTES-HA" />
<Type class="ND3P3A" element="N" mass="14.007" name="DGNTS-N" />
<Type class="DRUD" mass="0.0" name="Drude-DGNTS-N" />
<Type class="HDP1B" element="H" mass="1.008" name="DGNTS-HT1" />
<Type class="HDP1B" element="H" mass="1.008" name="DGNTS-HT2" />
<Type class="HDP1B" element="H" mass="1.008" name="DGNTS-HT3" />
<Type class="CD32C" element="C" mass="12.011" name="DGNTS-CA" />
<Type class="DRUD" mass="0.0" name="Drude-DGNTS-CA" />
<Type class="HDA2C" element="H" mass="1.008" name="DGNTS-HA1" />
<Type class="HDA2C" element="H" mass="1.008" name="DGNTS-HA2" />
<Type class="ND3P2A" element="N" mass="14.007" name="DPROP-N" /> <Type class="ND3P2A" element="N" mass="14.007" name="DPROP-N" />
<Type class="DRUD" mass="0.0" name="Drude-DPROP-N" /> <Type class="DRUD" mass="0.0" name="Drude-DPROP-N" />
<Type class="HDP1B" element="H" mass="1.008" name="DPROP-HT1" /> <Type class="HDP1B" element="H" mass="1.008" name="DPROP-HT1" />
...@@ -10169,6 +10148,17 @@ ...@@ -10169,6 +10148,17 @@
<Type class="LPD" mass="0.0" name="DCNEU-LPT2" /> <Type class="LPD" mass="0.0" name="DCNEU-LPT2" />
<Type class="LPD" mass="0.0" name="DCNEU-LPT3" /> <Type class="LPD" mass="0.0" name="DCNEU-LPT3" />
<Type class="LPD" mass="0.0" name="DCNEU-LPT4" /> <Type class="LPD" mass="0.0" name="DCNEU-LPT4" />
<Type class="CD2O3A" element="C" mass="12.011" name="DCNES-C" />
<Type class="DRUD" mass="0.0" name="Drude-DCNES-C" />
<Type class="OD2C3A" element="O" mass="15.9994" name="DCNES-OT1" />
<Type class="DRUD" mass="0.0" name="Drude-DCNES-OT1" />
<Type class="OD31F" element="O" mass="15.9994" name="DCNES-OT2" />
<Type class="DRUD" mass="0.0" name="Drude-DCNES-OT2" />
<Type class="HDP1A" element="H" mass="1.008" name="DCNES-HT" />
<Type class="LPD" mass="0.0" name="DCNES-LPT1" />
<Type class="LPD" mass="0.0" name="DCNES-LPT2" />
<Type class="LPD" mass="0.0" name="DCNES-LPT3" />
<Type class="LPD" mass="0.0" name="DCNES-LPT4" />
<Type class="ND2A2" element="N" mass="14.007" name="DCT1-N" /> <Type class="ND2A2" element="N" mass="14.007" name="DCT1-N" />
<Type class="DRUD" mass="0.0" name="Drude-DCT1-N" /> <Type class="DRUD" mass="0.0" name="Drude-DCT1-N" />
<Type class="HDP1A" element="H" mass="1.008" name="DCT1-HN" /> <Type class="HDP1A" element="H" mass="1.008" name="DCT1-HN" />
...@@ -10206,6 +10196,16 @@ ...@@ -10206,6 +10196,16 @@
<Type class="HDP1A" element="H" mass="1.008" name="DCT2-HTC2" /> <Type class="HDP1A" element="H" mass="1.008" name="DCT2-HTC2" />
<Type class="LPDO1" mass="0.0" name="DCT2-LPOA" /> <Type class="LPDO1" mass="0.0" name="DCT2-LPOA" />
<Type class="LPDO1" mass="0.0" name="DCT2-LPOB" /> <Type class="LPDO1" mass="0.0" name="DCT2-LPOB" />
<Type class="CD2O1A" element="C" mass="12.011" name="DCT2S-C" />
<Type class="DRUD" mass="0.0" name="Drude-DCT2S-C" />
<Type class="OD2C1A" element="O" mass="15.9994" name="DCT2S-O" />
<Type class="DRUD" mass="0.0" name="Drude-DCT2S-O" />
<Type class="ND2A1" element="N" mass="14.007" name="DCT2S-NT" />
<Type class="DRUD" mass="0.0" name="Drude-DCT2S-NT" />
<Type class="HDP1A" element="H" mass="1.008" name="DCT2S-HTC1" />
<Type class="HDP1A" element="H" mass="1.008" name="DCT2S-HTC2" />
<Type class="LPDO1" mass="0.0" name="DCT2S-LPOA" />
<Type class="LPDO1" mass="0.0" name="DCT2S-LPOB" />
<Type class="OD306A" element="O" mass="15.9994" name="OMEA-O5" /> <Type class="OD306A" element="O" mass="15.9994" name="OMEA-O5" />
<Type class="DRUD" mass="0.0" name="Drude-OMEA-O5" /> <Type class="DRUD" mass="0.0" name="Drude-OMEA-O5" />
<Type class="CD31HA" element="C" mass="12.011" name="OMEA-C1" /> <Type class="CD31HA" element="C" mass="12.011" name="OMEA-C1" />
...@@ -10414,10 +10414,8 @@ ...@@ -10414,10 +10414,8 @@
<AllowPatch name="ACE_3" /> <AllowPatch name="ACE_3" />
<AllowPatch name="CTER_1" /> <AllowPatch name="CTER_1" />
<AllowPatch name="CNEU_1" /> <AllowPatch name="CNEU_1" />
<AllowPatch name="CNES_1" />
<AllowPatch name="CT1_1" /> <AllowPatch name="CT1_1" />
<AllowPatch name="CT2_1" /> <AllowPatch name="CT2_1" />
<AllowPatch name="CT2S_2" />
<AllowPatch name="CT3_2" /> <AllowPatch name="CT3_2" />
</Residue> </Residue>
<Residue name="ALA"> <Residue name="ALA">
...@@ -10455,10 +10453,8 @@ ...@@ -10455,10 +10453,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="ARG"> <Residue name="ARG">
...@@ -10527,14 +10523,11 @@ ...@@ -10527,14 +10523,11 @@
<ExternalBond atomName="N" /> <ExternalBond atomName="N" />
<ExternalBond atomName="C" /> <ExternalBond atomName="C" />
<AllowPatch name="NTER_1" /> <AllowPatch name="NTER_1" />
<AllowPatch name="PROP_0" />
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="ASN"> <Residue name="ASN">
...@@ -10587,10 +10580,8 @@ ...@@ -10587,10 +10580,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="ASP"> <Residue name="ASP">
...@@ -10643,10 +10634,8 @@ ...@@ -10643,10 +10634,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
<AllowPatch name="ASPP_0" /> <AllowPatch name="ASPP_0" />
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...@@ -10692,10 +10681,8 @@ ...@@ -10692,10 +10681,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="GLN"> <Residue name="GLN">
...@@ -10755,10 +10742,8 @@ ...@@ -10755,10 +10742,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="GLU"> <Residue name="GLU">
...@@ -10818,10 +10803,8 @@ ...@@ -10818,10 +10803,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
<AllowPatch name="GLUP_0" /> <AllowPatch name="GLUP_0" />
</Residue> </Residue>
...@@ -10850,15 +10833,12 @@ ...@@ -10850,15 +10833,12 @@
<ExternalBond atomName="N" /> <ExternalBond atomName="N" />
<ExternalBond atomName="C" /> <ExternalBond atomName="C" />
<AllowPatch name="GNTE_0" /> <AllowPatch name="GNTE_0" />
<AllowPatch name="GNTS_1" />
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="GNNU_0" /> <AllowPatch name="GNNU_0" />
<AllowPatch name="CTEG_0" /> <AllowPatch name="CTEG_0" />
<AllowPatch name="CNEG_0" /> <AllowPatch name="CNEG_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1G_0" /> <AllowPatch name="CT1G_0" />
<AllowPatch name="CT2G_0" /> <AllowPatch name="CT2G_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="HSD"> <Residue name="HSD">
...@@ -10920,10 +10900,8 @@ ...@@ -10920,10 +10900,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
<AllowPatch name="HS2_0" /> <AllowPatch name="HS2_0" />
</Residue> </Residue>
...@@ -10987,10 +10965,8 @@ ...@@ -10987,10 +10965,8 @@
<AllowPatch name="NNEU_0" /> <AllowPatch name="NNEU_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="HSP"> <Residue name="HSP">
...@@ -11050,10 +11026,8 @@ ...@@ -11050,10 +11026,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="ILE"> <Residue name="ILE">
...@@ -11112,10 +11086,8 @@ ...@@ -11112,10 +11086,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="LEU"> <Residue name="LEU">
...@@ -11174,10 +11146,8 @@ ...@@ -11174,10 +11146,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="LYS"> <Residue name="LYS">
...@@ -11240,14 +11210,11 @@ ...@@ -11240,14 +11210,11 @@
<ExternalBond atomName="N" /> <ExternalBond atomName="N" />
<ExternalBond atomName="C" /> <ExternalBond atomName="C" />
<AllowPatch name="NTER_1" /> <AllowPatch name="NTER_1" />
<AllowPatch name="PROP_0" />
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
<AllowPatch name="LSN_0" /> <AllowPatch name="LSN_0" />
<AllowPatch name="KAC_0" /> <AllowPatch name="KAC_0" />
...@@ -11308,10 +11275,8 @@ ...@@ -11308,10 +11275,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="PHE"> <Residue name="PHE">
...@@ -11378,10 +11343,8 @@ ...@@ -11378,10 +11343,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="PRO"> <Residue name="PRO">
...@@ -11429,8 +11392,6 @@ ...@@ -11429,8 +11392,6 @@
<AllowPatch name="PROP_0" /> <AllowPatch name="PROP_0" />
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTEP_0" /> <AllowPatch name="CTEP_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="SER"> <Residue name="SER">
...@@ -11475,10 +11436,8 @@ ...@@ -11475,10 +11436,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
</Residue> </Residue>
<Residue name="THR"> <Residue name="THR">
...@@ -11530,10 +11489,8 @@ ...@@ -11530,10 +11489,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="TRP"> <Residue name="TRP">
...@@ -11612,10 +11569,8 @@ ...@@ -11612,10 +11569,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="TYR"> <Residue name="TYR">
...@@ -11689,10 +11644,8 @@ ...@@ -11689,10 +11644,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="VAL"> <Residue name="VAL">
...@@ -11744,10 +11697,8 @@ ...@@ -11744,10 +11697,8 @@
<AllowPatch name="ACE_0" /> <AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" /> <AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" /> <AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" /> <AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" /> <AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" /> <AllowPatch name="CT3_1" />
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<Residue name="ALLO"> <Residue name="ALLO">
...@@ -12742,7 +12693,6 @@ ...@@ -12742,7 +12693,6 @@
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<AllowPatch name="ACE_2" /> <AllowPatch name="ACE_2" />
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<AllowPatch name="CT3_0" /> <AllowPatch name="CT3_0" />
<AllowPatch name="OMEA_0" /> <AllowPatch name="OMEA_0" />
<AllowPatch name="1AOME_0" /> <AllowPatch name="1AOME_0" />
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...@@ -17472,7 +17409,6 @@ ...@@ -17472,7 +17409,6 @@
<VirtualSite atomName1="O" atomName2="C1" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LP1B" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="O" atomName2="C1" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LP1B" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPMA" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPMA" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPMB" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPMB" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" /> <AllowPatch name="CT3_0" />
</Residue> </Residue>
<Residue name="MPRO"> <Residue name="MPRO">
...@@ -17517,7 +17453,6 @@ ...@@ -17517,7 +17453,6 @@
<VirtualSite atomName1="O" atomName2="C1" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LP1B" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="O" atomName2="C1" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LP1B" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPMA" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPMA" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPMB" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPMB" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" /> <AllowPatch name="CT3_0" />
</Residue> </Residue>
<Residue name="MBU"> <Residue name="MBU">
...@@ -17569,7 +17504,6 @@ ...@@ -17569,7 +17504,6 @@
<VirtualSite atomName1="O" atomName2="C1" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LP1B" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="O" atomName2="C1" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LP1B" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPMA" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPMA" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPMB" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OM" atomName2="C2" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPMB" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" /> <AllowPatch name="CT3_0" />
</Residue> </Residue>
<Residue name="FETH"> <Residue name="FETH">
...@@ -17890,7 +17824,6 @@ ...@@ -17890,7 +17824,6 @@
<Bond atomName1="C" atomName2="H1" /> <Bond atomName1="C" atomName2="H1" />
<Bond atomName1="C" atomName2="H2" /> <Bond atomName1="C" atomName2="H2" />
<Bond atomName1="C" atomName2="H3" /> <Bond atomName1="C" atomName2="H3" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" /> <AllowPatch name="CT3_0" />
</Residue> </Residue>
<Residue name="ETO"> <Residue name="ETO">
...@@ -21560,39 +21493,6 @@ ...@@ -21560,39 +21493,6 @@
<RemoveBond atomName1="HN" atomName2="N" /> <RemoveBond atomName1="HN" atomName2="N" />
<RemoveExternalBond atomName="N" /> <RemoveExternalBond atomName="N" />
</Patch> </Patch>
<Patch name="GNTS_0">
<AddAtom charge="0.34" name="HT1" type="GNTS-HT1" />
<AddAtom charge="0.34" name="HT2" type="GNTS-HT2" />
<AddAtom charge="0.34" name="HT3" type="GNTS-HT3" />
<AddBond atomName1="HT1" atomName2="N" />
<AddBond atomName1="HT2" atomName2="N" />
<AddBond atomName1="HT3" atomName2="N" />
<ChangeAtom charge="2.276158038387988" name="CA" type="GNTS-CA" />
<ChangeAtom charge="-2.233158038387988" name="DCA" type="Drude-GNTS-CA" />
<ChangeAtom charge="-1.9770909072094385" name="DN" type="Drude-GNTS-N" />
<ChangeAtom charge="0.143" name="HA1" type="GNTS-HA1" />
<ChangeAtom charge="0.143" name="HA2" type="GNTS-HA2" />
<ChangeAtom charge="1.6280909072094385" name="N" type="GNTS-N" />
<RemoveAtom name="HN" />
<RemoveBond atomName1="HN" atomName2="N" />
</Patch>
<Patch name="GNTS_1">
<AddAtom charge="0.34" name="HT1" type="GNTS-HT1" />
<AddAtom charge="0.34" name="HT2" type="GNTS-HT2" />
<AddAtom charge="0.34" name="HT3" type="GNTS-HT3" />
<AddBond atomName1="HT1" atomName2="N" />
<AddBond atomName1="HT2" atomName2="N" />
<AddBond atomName1="HT3" atomName2="N" />
<ChangeAtom charge="2.276158038387988" name="CA" type="GNTS-CA" />
<ChangeAtom charge="-2.233158038387988" name="DCA" type="Drude-GNTS-CA" />
<ChangeAtom charge="-1.9770909072094385" name="DN" type="Drude-GNTS-N" />
<ChangeAtom charge="0.143" name="HA1" type="GNTS-HA1" />
<ChangeAtom charge="0.143" name="HA2" type="GNTS-HA2" />
<ChangeAtom charge="1.6280909072094385" name="N" type="GNTS-N" />
<RemoveAtom name="HN" />
<RemoveBond atomName1="HN" atomName2="N" />
<RemoveExternalBond atomName="N" />
</Patch>
<Patch name="PROP_0"> <Patch name="PROP_0">
<AddAtom charge="0.266" name="HT1" type="PROP-HT1" /> <AddAtom charge="0.266" name="HT1" type="PROP-HT1" />
<AddAtom charge="0.266" name="HT2" type="PROP-HT2" /> <AddAtom charge="0.266" name="HT2" type="PROP-HT2" />
...@@ -21978,57 +21878,6 @@ ...@@ -21978,57 +21878,6 @@
<VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPT3" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPT3" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPT4" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" /> <VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPT4" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
</Patch> </Patch>
<Patch name="CNES_0">
<AddAtom charge="-1.6663059805572336" name="DOT1" type="Drude-CNES-OT1" />
<AddAtom charge="-1.963334406026505" name="DOT2" type="Drude-CNES-OT2" />
<AddAtom charge="0.374" name="HT" type="CNES-HT" />
<AddAtom charge="-0.319" name="LPT1" type="CNES-LPT1" />
<AddAtom charge="-0.319" name="LPT2" type="CNES-LPT2" />
<AddAtom charge="-0.285" name="LPT3" type="CNES-LPT3" />
<AddAtom charge="-0.285" name="LPT4" type="CNES-LPT4" />
<AddAtom charge="1.6663059805572336" name="OT1" type="CNES-OT1" />
<AddAtom charge="1.963334406026505" name="OT2" type="CNES-OT2" />
<AddBond atomName1="C" atomName2="OT1" />
<AddBond atomName1="C" atomName2="OT2" />
<AddBond atomName1="HT" atomName2="OT2" />
<ChangeAtom charge="2.7405268573119237" name="C" type="CNES-C" />
<ChangeAtom charge="-1.9065268573119238" name="DC" type="Drude-CNES-C" />
<RemoveAtom name="DO" />
<RemoveAtom name="LPOA" />
<RemoveAtom name="LPOB" />
<RemoveAtom name="O" />
<RemoveBond atomName1="C" atomName2="O" />
<RemoveExternalBond atomName="C" />
<VirtualSite atomName1="OT1" atomName2="OT2" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPT1" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OT1" atomName2="OT2" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPT2" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPT3" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPT4" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
</Patch>
<Patch name="CNES_1">
<AddAtom charge="-1.6663059805572336" name="DOT1" type="Drude-CNES-OT1" />
<AddAtom charge="-1.963334406026505" name="DOT2" type="Drude-CNES-OT2" />
<AddAtom charge="0.374" name="HT" type="CNES-HT" />
<AddAtom charge="-0.319" name="LPT1" type="CNES-LPT1" />
<AddAtom charge="-0.319" name="LPT2" type="CNES-LPT2" />
<AddAtom charge="-0.285" name="LPT3" type="CNES-LPT3" />
<AddAtom charge="-0.285" name="LPT4" type="CNES-LPT4" />
<AddAtom charge="1.6663059805572336" name="OT1" type="CNES-OT1" />
<AddAtom charge="1.963334406026505" name="OT2" type="CNES-OT2" />
<AddBond atomName1="C" atomName2="OT1" />
<AddBond atomName1="C" atomName2="OT2" />
<AddBond atomName1="HT" atomName2="OT2" />
<ChangeAtom charge="2.7405268573119237" name="C" type="CNES-C" />
<ChangeAtom charge="-1.9065268573119238" name="DC" type="Drude-CNES-C" />
<RemoveAtom name="DO" />
<RemoveAtom name="LPOA" />
<RemoveAtom name="LPOB" />
<RemoveAtom name="O" />
<RemoveBond atomName1="C" atomName2="O" />
<VirtualSite atomName1="OT1" atomName2="OT2" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPT1" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OT1" atomName2="OT2" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPT2" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="0.03269217666591343" siteName="LPT3" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
<VirtualSite atomName1="OT2" atomName2="HT" atomName3="C" p1="-0.012485829976186883" p2="0.0005706440663482743" p3="-0.03269217666591343" siteName="LPT4" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.0" wx3="1.0" wy1="0" wy2="-1" wy3="1" />
</Patch>
<Patch name="CT1_0"> <Patch name="CT1_0">
<AddAtom charge="2.2962872001035097" name="CT" type="CT1-CT" /> <AddAtom charge="2.2962872001035097" name="CT" type="CT1-CT" />
<AddAtom charge="-2.3262872001035095" name="DCT" type="Drude-CT1-CT" /> <AddAtom charge="-2.3262872001035095" name="DCT" type="Drude-CT1-CT" />
...@@ -22211,51 +22060,6 @@ ...@@ -22211,51 +22060,6 @@
<ChangeAtom charge="1.6675290868987966" name="O" type="CT2G-O" /> <ChangeAtom charge="1.6675290868987966" name="O" type="CT2G-O" />
<RemoveExternalBond atomName="C" /> <RemoveExternalBond atomName="C" />
</Patch> </Patch>
<Patch name="CT2S_0">
<AddAtom charge="-2.2739161182852508" name="DNT" type="Drude-CT2S-NT" />
<AddAtom charge="0.303" name="HTC1" type="CT2S-HTC1" />
<AddAtom charge="0.351" name="HTC2" type="CT2S-HTC2" />
<AddAtom charge="-0.411" name="LPOA" type="CT2S-LPOA" />
<AddAtom charge="-0.264" name="LPOB" type="CT2S-LPOB" />
<AddAtom charge="1.4919161182852507" name="NT" type="CT2S-NT" />
<AddBond atomName1="C" atomName2="NT" />
<AddBond atomName1="HTC1" atomName2="NT" />
<AddBond atomName1="HTC2" atomName2="NT" />
<ChangeAtom charge="2.951382122346228" name="C" type="CT2S-C" />
<ChangeAtom charge="-2.1833821223462277" name="DC" type="Drude-CT2S-C" />
<ChangeAtom charge="-1.6325290868987967" name="DO" type="Drude-CT2S-O" />
<ChangeAtom charge="1.6675290868987966" name="O" type="CT2S-O" />
</Patch>
<Patch name="CT2S_1">
<AddAtom charge="-2.2739161182852508" name="DNT" type="Drude-CT2S-NT" />
<AddAtom charge="0.303" name="HTC1" type="CT2S-HTC1" />
<AddAtom charge="0.351" name="HTC2" type="CT2S-HTC2" />
<AddAtom charge="1.4919161182852507" name="NT" type="CT2S-NT" />
<AddBond atomName1="C" atomName2="NT" />
<AddBond atomName1="HTC1" atomName2="NT" />
<AddBond atomName1="HTC2" atomName2="NT" />
<ChangeAtom charge="2.951382122346228" name="C" type="CT2S-C" />
<ChangeAtom charge="-2.1833821223462277" name="DC" type="Drude-CT2S-C" />
<ChangeAtom charge="-1.6325290868987967" name="DO" type="Drude-CT2S-O" />
<ChangeAtom charge="-0.411" name="LPOA" type="CT2S-LPOA" />
<ChangeAtom charge="-0.264" name="LPOB" type="CT2S-LPOB" />
<ChangeAtom charge="1.6675290868987966" name="O" type="CT2S-O" />
<RemoveExternalBond atomName="C" />
</Patch>
<Patch name="CT2S_2">
<AddBond atomName1="HTC1" atomName2="NT" />
<AddBond atomName1="HTC2" atomName2="NT" />
<ChangeAtom charge="2.951382122346228" name="C" type="CT2S-C" />
<ChangeAtom charge="-2.1833821223462277" name="DC" type="Drude-CT2S-C" />
<ChangeAtom charge="-2.2739161182852508" name="DNT" type="Drude-CT2S-NT" />
<ChangeAtom charge="-1.6325290868987967" name="DO" type="Drude-CT2S-O" />
<ChangeAtom charge="0.303" name="HTC1" type="CT2S-HTC1" />
<ChangeAtom charge="0.351" name="HTC2" type="CT2S-HTC2" />
<ChangeAtom charge="-0.411" name="LPOA" type="CT2S-LPOA" />
<ChangeAtom charge="-0.264" name="LPOB" type="CT2S-LPOB" />
<ChangeAtom charge="1.4919161182852507" name="NT" type="CT2S-NT" />
<ChangeAtom charge="1.6675290868987966" name="O" type="CT2S-O" />
</Patch>
<Patch name="CT3_0"> <Patch name="CT3_0">
<AddAtom charge="2.166666003079377" name="CAT" type="CT3-CAT" /> <AddAtom charge="2.166666003079377" name="CAT" type="CT3-CAT" />
<AddAtom charge="-2.221666003079377" name="DCAT" type="Drude-CT3-CAT" /> <AddAtom charge="-2.221666003079377" name="DCAT" type="Drude-CT3-CAT" />
...@@ -30342,8 +30146,6 @@ ...@@ -30342,8 +30146,6 @@
<Particle charge="-2.233158038387988" polarizability="0.0016560000000000004" thole="0.895" type1="Drude-GNTE-CA" type2="GNTE-CA" /> <Particle charge="-2.233158038387988" polarizability="0.0016560000000000004" thole="0.895" type1="Drude-GNTE-CA" type2="GNTE-CA" />
<Particle charge="-1.3653205186135353" polarizability="0.0006190000000000002" thole="0.317" type1="Drude-GNTE-C" type2="GNTE-C" /> <Particle charge="-1.3653205186135353" polarizability="0.0006190000000000002" thole="0.317" type1="Drude-GNTE-C" type2="GNTE-C" />
<Particle charge="-1.3204701080914898" polarizability="0.0005790000000000001" thole="0.37" type1="Drude-GNTE-O" type2="GNTE-O" /> <Particle charge="-1.3204701080914898" polarizability="0.0005790000000000001" thole="0.37" type1="Drude-GNTE-O" type2="GNTE-O" />
<Particle charge="-1.9770909072094385" polarizability="0.0012980000000000003" thole="0.895" type1="Drude-GNTS-N" type2="GNTS-N" />
<Particle charge="-2.233158038387988" polarizability="0.0016560000000000004" thole="0.895" type1="Drude-GNTS-CA" type2="GNTS-CA" />
<Particle charge="-2.1104417974686633" polarizability="0.0014790000000000005" thole="0.111" type1="Drude-PROP-N" type2="PROP-N" /> <Particle charge="-2.1104417974686633" polarizability="0.0014790000000000005" thole="0.111" type1="Drude-PROP-N" type2="PROP-N" />
<Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-PROP-CD" type2="PROP-CD" /> <Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-PROP-CD" type2="PROP-CD" />
<Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-PROP-CA" type2="PROP-CA" /> <Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-PROP-CA" type2="PROP-CA" />
...@@ -30390,9 +30192,6 @@ ...@@ -30390,9 +30192,6 @@
<Particle charge="-1.9065268573119238" polarizability="0.0012070000000000004" thole="0.708" type1="Drude-CNEG-C" type2="CNEG-C" /> <Particle charge="-1.9065268573119238" polarizability="0.0012070000000000004" thole="0.708" type1="Drude-CNEG-C" type2="CNEG-C" />
<Particle charge="-1.6663059805572336" polarizability="0.0009220000000000003" thole="1.539" type1="Drude-CNEG-OT1" type2="CNEG-OT1" /> <Particle charge="-1.6663059805572336" polarizability="0.0009220000000000003" thole="1.539" type1="Drude-CNEG-OT1" type2="CNEG-OT1" />
<Particle charge="-1.963334406026505" polarizability="0.0012800000000000003" thole="1.124" type1="Drude-CNEG-OT2" type2="CNEG-OT2" /> <Particle charge="-1.963334406026505" polarizability="0.0012800000000000003" thole="1.124" type1="Drude-CNEG-OT2" type2="CNEG-OT2" />
<Particle charge="-1.9065268573119238" polarizability="0.0012070000000000004" thole="0.708" type1="Drude-CNES-C" type2="CNES-C" />
<Particle charge="-1.6663059805572336" polarizability="0.0009220000000000003" thole="1.539" type1="Drude-CNES-OT1" type2="CNES-OT1" />
<Particle charge="-1.963334406026505" polarizability="0.0012800000000000003" thole="1.124" type1="Drude-CNES-OT2" type2="CNES-OT2" />
<Particle charge="-2.4183207668819215" polarizability="0.0019420000000000004" thole="0.25" type1="Drude-CT1-N" type2="CT1-N" /> <Particle charge="-2.4183207668819215" polarizability="0.0019420000000000004" thole="0.25" type1="Drude-CT1-N" type2="CT1-N" />
<Particle charge="-1.700297471742985" polarizability="0.0009600000000000002" thole="1.078" type1="Drude-CT1-CA" type2="CT1-CA" /> <Particle charge="-1.700297471742985" polarizability="0.0009600000000000002" thole="1.078" type1="Drude-CT1-CA" type2="CT1-CA" />
<Particle charge="-2.031185446309965" polarizability="0.0013700000000000003" thole="1.747" type1="Drude-CT1-C" type2="CT1-C" /> <Particle charge="-2.031185446309965" polarizability="0.0013700000000000003" thole="1.747" type1="Drude-CT1-C" type2="CT1-C" />
...@@ -30415,9 +30214,6 @@ ...@@ -30415,9 +30214,6 @@
<Particle charge="-2.1833821223462277" polarizability="0.0015830000000000004" thole="1.095" type1="Drude-CT2G-C" type2="CT2G-C" /> <Particle charge="-2.1833821223462277" polarizability="0.0015830000000000004" thole="1.095" type1="Drude-CT2G-C" type2="CT2G-C" />
<Particle charge="-1.6325290868987967" polarizability="0.0008850000000000003" thole="1.227" type1="Drude-CT2G-O" type2="CT2G-O" /> <Particle charge="-1.6325290868987967" polarizability="0.0008850000000000003" thole="1.227" type1="Drude-CT2G-O" type2="CT2G-O" />
<Particle charge="-2.2739161182852508" polarizability="0.0017170000000000004" thole="1.132" type1="Drude-CT2G-NT" type2="CT2G-NT" /> <Particle charge="-2.2739161182852508" polarizability="0.0017170000000000004" thole="1.132" type1="Drude-CT2G-NT" type2="CT2G-NT" />
<Particle charge="-2.1833821223462277" polarizability="0.0015830000000000004" thole="1.095" type1="Drude-CT2S-C" type2="CT2S-C" />
<Particle charge="-1.6325290868987967" polarizability="0.0008850000000000003" thole="1.227" type1="Drude-CT2S-O" type2="CT2S-O" />
<Particle charge="-2.2739161182852508" polarizability="0.0017170000000000004" thole="1.132" type1="Drude-CT2S-NT" type2="CT2S-NT" />
<Particle charge="-2.4183207668819215" polarizability="0.0019420000000000004" thole="0.25" type1="Drude-CT3-NT" type2="CT3-NT" /> <Particle charge="-2.4183207668819215" polarizability="0.0019420000000000004" thole="0.25" type1="Drude-CT3-NT" type2="CT3-NT" />
<Particle charge="-2.221666003079377" polarizability="0.0016390000000000005" thole="2.122" type1="Drude-CT3-CAT" type2="CT3-CAT" /> <Particle charge="-2.221666003079377" polarizability="0.0016390000000000005" thole="2.122" type1="Drude-CT3-CAT" type2="CT3-CAT" />
<Particle charge="-2.5231425294508214" polarizability="0.0021140000000000004" thole="0.75" type1="Drude-ASPP-CB" type2="ASPP-CB" /> <Particle charge="-2.5231425294508214" polarizability="0.0021140000000000004" thole="0.75" type1="Drude-ASPP-CB" type2="ASPP-CB" />
...@@ -30447,6 +30243,8 @@ ...@@ -30447,6 +30243,8 @@
<Particle charge="-1.3204701080914898" polarizability="0.0005790000000000001" thole="0.37" type1="Drude-DNTER-O" type2="DNTER-O" /> <Particle charge="-1.3204701080914898" polarizability="0.0005790000000000001" thole="0.37" type1="Drude-DNTER-O" type2="DNTER-O" />
<Particle charge="-1.9770909072094385" polarizability="0.0012980000000000003" thole="0.895" type1="Drude-DNTES-N" type2="DNTES-N" /> <Particle charge="-1.9770909072094385" polarizability="0.0012980000000000003" thole="0.895" type1="Drude-DNTES-N" type2="DNTES-N" />
<Particle charge="-2.233158038387988" polarizability="0.0016560000000000004" thole="0.895" type1="Drude-DNTES-CA" type2="DNTES-CA" /> <Particle charge="-2.233158038387988" polarizability="0.0016560000000000004" thole="0.895" type1="Drude-DNTES-CA" type2="DNTES-CA" />
<Particle charge="-1.9770909072094385" polarizability="0.0012980000000000003" thole="0.895" type1="Drude-DGNTS-N" type2="DGNTS-N" />
<Particle charge="-2.233158038387988" polarizability="0.0016560000000000004" thole="0.895" type1="Drude-DGNTS-CA" type2="DGNTS-CA" />
<Particle charge="-2.1104417974686633" polarizability="0.0014790000000000005" thole="0.111" type1="Drude-DPROP-N" type2="DPROP-N" /> <Particle charge="-2.1104417974686633" polarizability="0.0014790000000000005" thole="0.111" type1="Drude-DPROP-N" type2="DPROP-N" />
<Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-DPROP-CD" type2="DPROP-CD" /> <Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-DPROP-CD" type2="DPROP-CD" />
<Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-DPROP-CA" type2="DPROP-CA" /> <Particle charge="-2.179931223836688" polarizability="0.0015780000000000004" thole="1.429" type1="Drude-DPROP-CA" type2="DPROP-CA" />
...@@ -30479,6 +30277,9 @@ ...@@ -30479,6 +30277,9 @@
<Particle charge="-1.9065268573119238" polarizability="0.0012070000000000004" thole="0.708" type1="Drude-DCNEU-C" type2="DCNEU-C" /> <Particle charge="-1.9065268573119238" polarizability="0.0012070000000000004" thole="0.708" type1="Drude-DCNEU-C" type2="DCNEU-C" />
<Particle charge="-1.6663059805572336" polarizability="0.0009220000000000003" thole="1.539" type1="Drude-DCNEU-OT1" type2="DCNEU-OT1" /> <Particle charge="-1.6663059805572336" polarizability="0.0009220000000000003" thole="1.539" type1="Drude-DCNEU-OT1" type2="DCNEU-OT1" />
<Particle charge="-1.963334406026505" polarizability="0.0012800000000000003" thole="1.124" type1="Drude-DCNEU-OT2" type2="DCNEU-OT2" /> <Particle charge="-1.963334406026505" polarizability="0.0012800000000000003" thole="1.124" type1="Drude-DCNEU-OT2" type2="DCNEU-OT2" />
<Particle charge="-1.9065268573119238" polarizability="0.0012070000000000004" thole="0.708" type1="Drude-DCNES-C" type2="DCNES-C" />
<Particle charge="-1.6663059805572336" polarizability="0.0009220000000000003" thole="1.539" type1="Drude-DCNES-OT1" type2="DCNES-OT1" />
<Particle charge="-1.963334406026505" polarizability="0.0012800000000000003" thole="1.124" type1="Drude-DCNES-OT2" type2="DCNES-OT2" />
<Particle charge="-2.4183207668819215" polarizability="0.0019420000000000004" thole="0.25" type1="Drude-DCT1-N" type2="DCT1-N" /> <Particle charge="-2.4183207668819215" polarizability="0.0019420000000000004" thole="0.25" type1="Drude-DCT1-N" type2="DCT1-N" />
<Particle charge="-1.700297471742985" polarizability="0.0009600000000000002" thole="1.078" type1="Drude-DCT1-CA" type2="DCT1-CA" /> <Particle charge="-1.700297471742985" polarizability="0.0009600000000000002" thole="1.078" type1="Drude-DCT1-CA" type2="DCT1-CA" />
<Particle charge="-2.031185446309965" polarizability="0.0013700000000000003" thole="1.747" type1="Drude-DCT1-C" type2="DCT1-C" /> <Particle charge="-2.031185446309965" polarizability="0.0013700000000000003" thole="1.747" type1="Drude-DCT1-C" type2="DCT1-C" />
...@@ -30490,6 +30291,9 @@ ...@@ -30490,6 +30291,9 @@
<Particle charge="-2.1833821223462277" polarizability="0.0015830000000000004" thole="1.095" type1="Drude-DCT2-C" type2="DCT2-C" /> <Particle charge="-2.1833821223462277" polarizability="0.0015830000000000004" thole="1.095" type1="Drude-DCT2-C" type2="DCT2-C" />
<Particle charge="-1.6325290868987967" polarizability="0.0008850000000000003" thole="1.227" type1="Drude-DCT2-O" type2="DCT2-O" /> <Particle charge="-1.6325290868987967" polarizability="0.0008850000000000003" thole="1.227" type1="Drude-DCT2-O" type2="DCT2-O" />
<Particle charge="-2.2739161182852508" polarizability="0.0017170000000000004" thole="1.132" type1="Drude-DCT2-NT" type2="DCT2-NT" /> <Particle charge="-2.2739161182852508" polarizability="0.0017170000000000004" thole="1.132" type1="Drude-DCT2-NT" type2="DCT2-NT" />
<Particle charge="-2.1833821223462277" polarizability="0.0015830000000000004" thole="1.095" type1="Drude-DCT2S-C" type2="DCT2S-C" />
<Particle charge="-1.6325290868987967" polarizability="0.0008850000000000003" thole="1.227" type1="Drude-DCT2S-O" type2="DCT2S-O" />
<Particle charge="-2.2739161182852508" polarizability="0.0017170000000000004" thole="1.132" type1="Drude-DCT2S-NT" type2="DCT2S-NT" />
<Particle charge="-1.233204161452102" polarizability="0.0005050000000000001" thole="0.907" type1="Drude-OMEA-O5" type2="OMEA-O5" /> <Particle charge="-1.233204161452102" polarizability="0.0005050000000000001" thole="0.907" type1="Drude-OMEA-O5" type2="OMEA-O5" />
<Particle charge="-1.7353588402977551" polarizability="0.0010000000000000002" thole="0.487" type1="Drude-OMEA-C1" type2="OMEA-C1" /> <Particle charge="-1.7353588402977551" polarizability="0.0010000000000000002" thole="0.487" type1="Drude-OMEA-C1" type2="OMEA-C1" />
<Particle charge="-1.230759750403621" polarizability="0.0005030000000000001" thole="0.443" type1="Drude-OMEA-O1" type2="OMEA-O1" /> <Particle charge="-1.230759750403621" polarizability="0.0005030000000000001" thole="0.443" type1="Drude-OMEA-O1" type2="OMEA-O1" />
...@@ -30510,15 +30314,556 @@ ...@@ -30510,15 +30314,556 @@
import math import math
import openmm import openmm
   
residue_impropers = {'ALAD': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'HN')), ((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'C'), (0, 'CAT'), (0, 'HNT'))), 'ALA': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'ARG': (((0, 'CZ'), (0, 'NH1'), (0, 'NH2'), (0, 'NE')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'ASN': (((0, 'CG'), (0, 'CB'), (0, 'ND2'), (0, 'OD1')), ((0, 'ND2'), (0, 'HD21'), (0, 'HD22'), (0, 'CG')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'ASP': (((0, 'OD1'), (0, 'CB'), (0, 'OD2'), (0, 'CG')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'CYS': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'GLN': (((0, 'CD'), (0, 'CG'), (0, 'NE2'), (0, 'OE1')), ((0, 'NE2'), (0, 'HE21'), (0, 'HE22'), (0, 'CD')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'GLU': (((0, 'OE1'), (0, 'CG'), (0, 'OE2'), (0, 'CD')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'GLY': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'HSD': (((0, 'ND1'), (0, 'CG'), (0, 'CE1'), (0, 'HD1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'HSE': (((0, 'NE2'), (0, 'CD2'), (0, 'CE1'), (0, 'HE2')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'HSP': (((0, 'ND1'), (0, 'CE1'), (0, 'CG'), (0, 'HD1')), ((0, 'NE2'), (0, 'CE1'), (0, 'CD2'), (0, 'HE2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'ILE': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'LEU': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'LYS': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'MET': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'PHE': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'PRO': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'CD'))), 'SER': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'THR': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'TRP': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))), 'TYR': 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residue_impropers = {
patch_impropers = {'ACE': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'HN'))), 'ACP': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'CD'))), 'CTER': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),), 'CTEG': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),), 'CTEP': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),), 'CNEU': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),), 'CNEG': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),), 'CNES': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),), 'CT1': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),), 'CT1G': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),), 'CT2': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))), 'CT2G': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))), 'CT2S': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))), 'CT3': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'C'), (0, 'CAT'), (0, 'HNT'))), 'LINK': (((0, '3N'), (0, '2C'), (0, '3CA'), (0, '3HN')), ((0, '2C'), (0, '2CA'), (0, '3N'), (0, '2O'))), 'HS2': (((0, 'NE2'), (0, 'CD2'), (0, 'CE1'), (0, 'HE2')),), 'KAC': (((0, 'NZ'), (0, 'CH'), (0, 'CE'), (0, 'HZ')), ((0, 'CH'), (0, 'CH3'), (0, 'NZ'), (0, 'OH'))), 'DACE': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'HN'))), 'DACP': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'CD'))), 'DCTER': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),), 'DCTEG': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),), 'DCTEP': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),), 'DCTES': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),), 'DCNEU': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),), 'DCNEG': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),), 'DCNES': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),), 'DCT1': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),), 'DCT1G': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),), 'DCT2': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))), 'DCT2G': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))), 'DCT2S': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))), 'DCT3': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'C'), (0, 'CAT'), (0, 'HNT')))} 'ALAD': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'HN')), ((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'C'), (0, 'CAT'), (0, 'HNT'))),
delete_impropers = {} 'ALA': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'ARG': (((0, 'CZ'), (0, 'NH1'), (0, 'NH2'), (0, 'NE')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'ASN': (((0, 'CG'), (0, 'CB'), (0, 'ND2'), (0, 'OD1')), ((0, 'ND2'), (0, 'HD21'), (0, 'HD22'), (0, 'CG')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'ASP': (((0, 'OD1'), (0, 'CB'), (0, 'OD2'), (0, 'CG')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'CYS': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'GLN': (((0, 'CD'), (0, 'CG'), (0, 'NE2'), (0, 'OE1')), ((0, 'NE2'), (0, 'HE21'), (0, 'HE22'), (0, 'CD')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'GLU': (((0, 'OE1'), (0, 'CG'), (0, 'OE2'), (0, 'CD')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'GLY': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'HSD': (((0, 'ND1'), (0, 'CG'), (0, 'CE1'), (0, 'HD1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'HSE': (((0, 'NE2'), (0, 'CD2'), (0, 'CE1'), (0, 'HE2')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'HSP': (((0, 'ND1'), (0, 'CE1'), (0, 'CG'), (0, 'HD1')), ((0, 'NE2'), (0, 'CE1'), (0, 'CD2'), (0, 'HE2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'ILE': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'LEU': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'LYS': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'MET': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'PHE': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'PRO': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'CD'))),
'SER': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'THR': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'TRP': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'TYR': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'VAL': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'ALDD': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'HN')), ((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'C'), (0, 'CAT'), (0, 'HNT'))),
'DALA': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DARG': (((0, 'CZ'), (0, 'NH1'), (0, 'NH2'), (0, 'NE')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DASN': (((0, 'CG'), (0, 'CB'), (0, 'ND2'), (0, 'OD1')), ((0, 'ND2'), (0, 'HD21'), (0, 'HD22'), (0, 'CG')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DASP': (((0, 'OD1'), (0, 'CB'), (0, 'OD2'), (0, 'CG')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DCYS': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DGLN': (((0, 'CD'), (0, 'CG'), (0, 'NE2'), (0, 'OE1')), ((0, 'NE2'), (0, 'HE21'), (0, 'HE22'), (0, 'CD')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DGLU': (((0, 'OE1'), (0, 'CG'), (0, 'OE2'), (0, 'CD')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DGLY': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DHSD': (((0, 'ND1'), (0, 'CG'), (0, 'CE1'), (0, 'HD1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DHSE': (((0, 'NE2'), (0, 'CD2'), (0, 'CE1'), (0, 'HE2')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DHSP': (((0, 'ND1'), (0, 'CE1'), (0, 'CG'), (0, 'HD1')), ((0, 'NE2'), (0, 'CE1'), (0, 'CD2'), (0, 'HE2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DILE': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DLEU': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DLYS': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DMET': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DPHE': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DPRO': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'CD'))),
'DSER': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DTHR': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DTRP': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DTYR': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'DVAL': (((0, 'C'), (0, 'CA'), (1, 'N'), (0, 'O')), ((0, 'N'), (-1, 'C'), (0, 'CA'), (0, 'HN'))),
'ALLO': (((0, 'C1'), (0, 'H1'), (0, 'C2'), (0, 'O1')),),
'PSIC': (((0, 'C2'), (0, 'C1'), (0, 'C3'), (0, 'O2')),),
'AGALA': (((0, 'C6'), (0, 'C5'), (0, 'O62'), (0, 'O61')),),
'BGALA': (((0, 'C6'), (0, 'C5'), (0, 'O62'), (0, 'O61')),),
'AGLCA': (((0, 'C6'), (0, 'C5'), (0, 'O62'), (0, 'O61')),),
'BGLCA': (((0, 'C6'), (0, 'C5'), (0, 'O62'), (0, 'O61')),),
'AIDOA': (((0, 'C6'), (0, 'C5'), (0, 'O62'), (0, 'O61')),),
'BIDOA': (((0, 'C6'), (0, 'C5'), (0, 'O62'), (0, 'O61')),),
'AGLCNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'BGLCNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'AGALNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'BGALNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'AMANNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'BMANNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'ARHMNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'BRHMNA': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C2'), (0, 'HN'))),
'ANE5AC': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C5'), (0, 'HN')), ((0, 'C1'), (0, 'C2'), (0, 'O12'), (0, 'O11'))),
'BNE5AC': (((0, 'C'), (0, 'CT'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'C5'), (0, 'HN')), ((0, 'C1'), (0, 'C2'), (0, 'O12'), (0, 'O11'))),
'2BTE': (((0, 'C2'), (0, 'C3'), (0, 'C1'), (0, 'H2')), ((0, 'C3'), (0, 'C2'), (0, 'C4'), (0, 'H3'))),
'2BTD': (((0, 'C2'), (0, 'C3'), (0, 'C1'), (0, 'H2')), ((0, 'C3'), (0, 'C2'), (0, 'C4'), (0, 'H3'))),
'2PTE': (((0, 'C3'), (0, 'C2'), (0, 'C4'), (0, 'H3')), ((0, 'C2'), (0, 'C3'), (0, 'C1'), (0, 'H2'))),
'2PTD': (((0, 'C3'), (0, 'C2'), (0, 'C4'), (0, 'H3')), ((0, 'C2'), (0, 'C3'), (0, 'C1'), (0, 'H2'))),
'2HEX': (((0, 'C2'), (0, 'C3'), (0, 'C1'), (0, 'H2')), ((0, 'C3'), (0, 'C2'), (0, 'C4'), (0, 'H3'))),
'2HED': (((0, 'C2'), (0, 'C3'), (0, 'C1'), (0, 'H2')), ((0, 'C3'), (0, 'C2'), (0, 'C4'), (0, 'H3'))),
'3HEX': (((0, 'C3'), (0, 'C4'), (0, 'C2'), (0, 'H3')), ((0, 'C4'), (0, 'C3'), (0, 'C5'), (0, 'H4'))),
'3HED': (((0, 'C3'), (0, 'C4'), (0, 'C2'), (0, 'H3')), ((0, 'C4'), (0, 'C3'), (0, 'C5'), (0, 'H4'))),
'5DEC': (((0, 'C5'), (0, 'C4'), (0, 'C6'), (0, 'H5')), ((0, 'C6'), (0, 'C5'), (0, 'C7'), (0, 'H6'))),
'5DED': (((0, 'C5'), (0, 'C4'), (0, 'C6'), (0, 'H5')), ((0, 'C6'), (0, 'C5'), (0, 'C7'), (0, 'H6'))),
'AALD': (((0, 'C'), (0, 'HA'), (0, 'CB'), (0, 'O')),),
'PALD': (((0, 'C'), (0, 'HA'), (0, 'CB'), (0, 'O')),),
'BALD': (((0, 'C'), (0, 'HA'), (0, 'CB'), (0, 'O')),),
'IBLD': (((0, 'C'), (0, 'HA'), (0, 'CB'), (0, 'O')),),
'ACO': (((0, 'C1'), (0, 'C2'), (0, 'C3'), (0, 'O1')),),
'BTON': (((0, 'C1'), (0, 'C2'), (0, 'C3'), (0, 'O1')),),
'FORM': (((0, 'C'), (0, 'N'), (0, 'O'), (0, 'HA')),),
'ACEM': (((0, 'C'), (0, 'CL'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'HC'), (0, 'HT'), (0, 'C'))),
'NMA': (((0, 'C'), (0, 'CL'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'CC'), (0, 'H'))),
'NEA': (((0, 'C'), (0, 'CL'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'CC'), (0, 'H'))),
'NPA': (((0, 'C'), (0, 'CL'), (0, 'N'), (0, 'O')), ((0, 'N'), (0, 'C'), (0, 'CC'), (0, 'H'))),
'DMA': (((0, 'C'), (0, 'CL'), (0, 'N'), (0, 'O')),),
'IMID': (((0, 'ND1'), (0, 'CG'), (0, 'CE1'), (0, 'HD1')), ((0, 'ND1'), (0, 'CE1'), (0, 'CG'), (0, 'HD1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CD2'), (0, 'NE2'), (0, 'CG'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'CE1'), (0, 'NE2'), (0, 'ND1'), (0, 'HE1')), ((0, 'CG'), (0, 'CD2'), (0, 'ND1'), (0, 'HG')), ((0, 'CG'), (0, 'ND1'), (0, 'CD2'), (0, 'HG'))),
'4MIM': (((0, 'ND1'), (0, 'CG'), (0, 'CE1'), (0, 'HD1')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1'))),
'4MIE': (((0, 'NE2'), (0, 'CD2'), (0, 'CE1'), (0, 'HE2')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1'))),
'INDO': (((0, 'HZ2'), (0, 'CH2'), (0, 'CE2'), (0, 'CZ2')), ((0, 'HZ2'), (0, 'CE2'), (0, 'CH2'), (0, 'CZ2')), ((0, 'HE3'), (0, 'CD2'), (0, 'CZ3'), (0, 'CE3')), ((0, 'HE3'), (0, 'CZ3'), (0, 'CD2'), (0, 'CE3')), ((0, 'HG'), (0, 'CD2'), (0, 'CD1'), (0, 'CG')), ((0, 'HG'), (0, 'CD1'), (0, 'CD2'), (0, 'CG')), ((0, 'HD1'), (0, 'CG'), (0, 'NE1'), (0, 'CD1')), ((0, 'HD1'), (0, 'NE1'), (0, 'CG'), (0, 'CD1')), ((0, 'HE1'), (0, 'CE2'), (0, 'CD1'), (0, 'NE1')), ((0, 'HE1'), (0, 'CD1'), (0, 'CE2'), (0, 'NE1'))),
'PUR0': (((0, 'N9'), (0, 'C4'), (0, 'C8'), (0, 'H9')), ((0, 'N9'), (0, 'C8'), (0, 'C4'), (0, 'H9')), ((0, 'C8'), (0, 'N9'), (0, 'N7'), (0, 'H8')), ((0, 'C8'), (0, 'N7'), (0, 'N9'), (0, 'H8')), ((0, 'C5'), (0, 'C4'), (0, 'C6'), (0, 'N7')), ((0, 'C5'), (0, 'C6'), (0, 'C4'), (0, 'N7')), ((0, 'C4'), (0, 'C5'), (0, 'N3'), (0, 'N9')), ((0, 'C4'), (0, 'N3'), (0, 'C5'), (0, 'N9'))),
'PUR1': (((0, 'N9'), (0, 'C5'), (0, 'C8'), (0, 'H9')), ((0, 'N9'), (0, 'C8'), (0, 'C5'), (0, 'H9')), ((0, 'C8'), (0, 'N9'), (0, 'N7'), (0, 'H8')), ((0, 'C8'), (0, 'N7'), (0, 'N9'), (0, 'H8')), ((0, 'C5'), (0, 'C4'), (0, 'C6'), (0, 'N9')), ((0, 'C5'), (0, 'C6'), (0, 'C4'), (0, 'N9')), ((0, 'C4'), (0, 'C5'), (0, 'N3'), (0, 'N7')), ((0, 'C4'), (0, 'N3'), (0, 'C5'), (0, 'N7'))),
'MIND': (((0, 'HZ2'), (0, 'CH2'), (0, 'CE2'), (0, 'CZ2')), ((0, 'HZ2'), (0, 'CE2'), (0, 'CH2'), (0, 'CZ2')), ((0, 'HE3'), (0, 'CD2'), (0, 'CZ3'), (0, 'CE3')), ((0, 'HE3'), (0, 'CZ3'), (0, 'CD2'), (0, 'CE3')), ((0, 'HD1'), (0, 'CG'), (0, 'NE1'), (0, 'CD1')), ((0, 'HD1'), (0, 'NE1'), (0, 'CG'), (0, 'CD1')), ((0, 'HE1'), (0, 'CE2'), (0, 'CD1'), (0, 'NE1')), ((0, 'HE1'), (0, 'CD1'), (0, 'CE2'), (0, 'NE1'))),
'ACET': (((0, 'O1'), (0, 'C1'), (0, 'O2'), (0, 'C2')),),
'GUAN': (((0, 'C'), (0, 'N2'), (0, 'N1'), (0, 'N3')),),
'MGUAN': (((0, 'C'), (0, 'N2'), (0, 'N1'), (0, 'N3')),),
'BGUAN': (((0, 'CZ'), (0, 'NH1'), (0, 'NH2'), (0, 'NE')),),
'IMIM': (((0, 'ND1'), (0, 'CE1'), (0, 'CG'), (0, 'HD1')), ((0, 'NE2'), (0, 'CE1'), (0, 'CD2'), (0, 'HE2')), ((0, 'CE1'), (0, 'ND1'), (0, 'NE2'), (0, 'HE1')), ((0, 'CG'), (0, 'CD2'), (0, 'ND1'), (0, 'HG')), ((0, 'CD2'), (0, 'CG'), (0, 'NE2'), (0, 'HD2'))),
'ACEH': (((0, 'O2'), (0, 'C1'), (0, 'O1'), (0, 'C2')),),
'MAS': (((0, 'O'), (0, 'C1'), (0, 'OM'), (0, 'C')),),
'EAS': (((0, 'O'), (0, 'C1'), (0, 'OM'), (0, 'C')),),
'MPRO': (((0, 'O'), (0, 'C1'), (0, 'OM'), (0, 'C')),),
'MBU': (((0, 'O'), (0, 'C1'), (0, 'OM'), (0, 'C')),),
'GLYC': (((0, 'O6'), (0, 'C7'), (0, 'O4'), (0, 'C5')), ((0, 'O10'), (0, 'C11'), (0, 'O8'), (0, 'C9'))),
'GLYP': (((0, 'O6'), (0, 'C7'), (0, 'O4'), (0, 'C5')), ((0, 'O10'), (0, 'C11'), (0, 'O8'), (0, 'C9'))),
'PRPC': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32'))),
'DMPC': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32'))),
'DPPC': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32'))),
'DSPC': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32'))),
'DOPC': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32')), ((0, 'C29'), (0, 'C210'), (0, 'C28'), (0, 'H9R')), ((0, 'C210'), (0, 'C29'), (0, 'C211'), (0, 'H10R')), ((0, 'C39'), (0, 'C310'), (0, 'C38'), (0, 'H9X')), ((0, 'C310'), (0, 'C39'), (0, 'C311'), (0, 'H10X'))),
'DLPE': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32'))),
'DPPE': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32'))),
'POPC': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32')), ((0, 'C29'), (0, 'C210'), (0, 'C28'), (0, 'H91')), ((0, 'C210'), (0, 'C29'), (0, 'C211'), (0, 'H101'))),
'DOPE': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32')), ((0, 'C29'), (0, 'C210'), (0, 'C28'), (0, 'H9R')), ((0, 'C210'), (0, 'C29'), (0, 'C211'), (0, 'H10R')), ((0, 'C39'), (0, 'C310'), (0, 'C38'), (0, 'H9X')), ((0, 'C310'), (0, 'C39'), (0, 'C311'), (0, 'H10X'))),
'POPE': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32')), ((0, 'C29'), (0, 'C210'), (0, 'C28'), (0, 'H91')), ((0, 'C210'), (0, 'C29'), (0, 'C211'), (0, 'H101'))),
'DLPC': (((0, 'C21'), (0, 'O21'), (0, 'C22'), (0, 'O22')), ((0, 'C31'), (0, 'O31'), (0, 'C32'), (0, 'O32'))),
}
patch_impropers = {
'ACE': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'HN'))),
'ACP': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'CD'))),
'CTER': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),),
'CTEG': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),),
'CTEP': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),),
'CNEU': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),),
'CNEG': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),),
'CT1': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),),
'CT1G': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),),
'CT2': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))),
'CT2G': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))),
'CT3': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'C'), (0, 'CAT'), (0, 'HNT'))),
'LINK': (((0, '3N'), (0, '2C'), (0, '3CA'), (0, '3HN')), ((0, '2C'), (0, '2CA'), (0, '3N'), (0, '2O'))),
'HS2': (((0, 'NE2'), (0, 'CD2'), (0, 'CE1'), (0, 'HE2')),),
'KAC': (((0, 'NZ'), (0, 'CH'), (0, 'CE'), (0, 'HZ')), ((0, 'CH'), (0, 'CH3'), (0, 'NZ'), (0, 'OH'))),
'DACE': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'HN'))),
'DACP': (((0, 'CY'), (0, 'CAY'), (0, 'N'), (0, 'OY')), ((0, 'N'), (0, 'CY'), (0, 'CA'), (0, 'CD'))),
'DCTER': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),),
'DCTEG': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),),
'DCTEP': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),),
'DCTES': (((0, 'C'), (0, 'OT1'), (0, 'OT2'), (0, 'CA')),),
'DCNEU': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),),
'DCNEG': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),),
'DCNES': (((0, 'OT1'), (0, 'CA'), (0, 'OT2'), (0, 'C')),),
'DCT1': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),),
'DCT1G': (((0, 'C'), (0, 'OT2'), (0, 'CA'), (0, 'OT1')),),
'DCT2': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))),
'DCT2G': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))),
'DCT2S': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'HTC1'), (0, 'HTC2'), (0, 'C'))),
'DCT3': (((0, 'C'), (0, 'CA'), (0, 'NT'), (0, 'O')), ((0, 'NT'), (0, 'C'), (0, 'CAT'), (0, 'HNT'))),
}
delete_impropers = {
}
residue_order = {
'ALAD': 0,
'ALA': 1,
'ARG': 2,
'ASN': 3,
'ASP': 4,
'CYS': 5,
'GLN': 6,
'GLU': 7,
'GLY': 8,
'HSD': 9,
'HSE': 10,
'HSP': 11,
'ILE': 12,
'LEU': 13,
'LYS': 14,
'MET': 15,
'PHE': 16,
'PRO': 17,
'SER': 18,
'THR': 19,
'TRP': 20,
'TYR': 21,
'VAL': 22,
'ALDD': 23,
'DALA': 24,
'DARG': 25,
'DASN': 26,
'DASP': 27,
'DCYS': 28,
'DGLN': 29,
'DGLU': 30,
'DGLY': 31,
'DHSD': 32,
'DHSE': 33,
'DHSP': 34,
'DILE': 35,
'DLEU': 36,
'DLYS': 37,
'DMET': 38,
'DPHE': 39,
'DPRO': 40,
'DSER': 41,
'DTHR': 42,
'DTRP': 43,
'DTYR': 44,
'DVAL': 45,
'ALLO': 46,
'PSIC': 47,
'AGALA': 48,
'BGALA': 49,
'AGLCA': 50,
'BGLCA': 51,
'AIDOA': 52,
'BIDOA': 53,
'AGLCNA': 54,
'BGLCNA': 55,
'AGALNA': 56,
'BGALNA': 57,
'AMANNA': 58,
'BMANNA': 59,
'ARHMNA': 60,
'BRHMNA': 61,
'ANE5AC': 62,
'BNE5AC': 63,
'2BTE': 64,
'2BTD': 65,
'2PTE': 66,
'2PTD': 67,
'2HEX': 68,
'2HED': 69,
'3HEX': 70,
'3HED': 71,
'5DEC': 72,
'5DED': 73,
'AALD': 74,
'PALD': 75,
'BALD': 76,
'IBLD': 77,
'ACO': 78,
'BTON': 79,
'FORM': 80,
'ACEM': 81,
'NMA': 82,
'NEA': 83,
'NPA': 84,
'DMA': 85,
'IMID': 86,
'4MIM': 87,
'4MIE': 88,
'INDO': 89,
'PUR0': 90,
'PUR1': 91,
'MIND': 92,
'ACET': 93,
'GUAN': 94,
'MGUAN': 95,
'BGUAN': 96,
'IMIM': 97,
'ACEH': 98,
'MAS': 99,
'EAS': 100,
'MPRO': 101,
'MBU': 102,
'GLYC': 103,
'GLYP': 104,
'PRPC': 105,
'DMPC': 106,
'DPPC': 107,
'DSPC': 108,
'DOPC': 109,
'DLPE': 110,
'DPPE': 111,
'POPC': 112,
'DOPE': 113,
'POPE': 114,
'DLPC': 115,
}
patch_order = {
'ACE': 0,
'ACP': 1,
'CTER': 2,
'CTEG': 3,
'CTEP': 4,
'CNEU': 5,
'CNEG': 6,
'CT1': 7,
'CT1G': 8,
'CT2': 9,
'CT2G': 10,
'CT3': 11,
'LINK': 12,
'HS2': 13,
'KAC': 14,
'DACE': 15,
'DACP': 16,
'DCTER': 17,
'DCTEG': 18,
'DCTEP': 19,
'DCTES': 20,
'DCNEU': 21,
'DCNEG': 22,
'DCNES': 23,
'DCT1': 24,
'DCT1G': 25,
'DCT2': 26,
'DCT2G': 27,
'DCT2S': 28,
'DCT3': 29,
}
periodic_improper_types = {
}
harmonic_improper_types = {
('OD2C3A', 'CD32C', 'OD31F', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD31F', 'CD32C', 'OD2C3A'): ((355.64, 0.0),),
('CD2O1A', 'CD32A', 'ND2A2', 'OD2C1A'): ((418.40000000000003, 0.0),),
('OD2C1A', 'ND2A2', 'CD32A', 'CD2O1A'): ((418.40000000000003, 0.0),),
('CD2O1A', 'CD31C', 'ND3A3', 'OD2C1A'): ((0.0, 0.0),),
('OD2C1A', 'ND3A3', 'CD31C', 'CD2O1A'): ((0.0, 0.0),),
('CD2O1A', 'CD32C', 'ND3A3', 'OD2C1A'): ((0.0, 0.0),),
('OD2C1A', 'ND3A3', 'CD32C', 'CD2O1A'): ((0.0, 0.0),),
('ND3A3', 'CD2O1A', 'CD31C', 'CD32A'): ((0.0, 0.0),),
('CD32A', 'CD31C', 'CD2O1A', 'ND3A3'): ((0.0, 0.0),),
('CD2O1A', 'CD31C', 'ND2A1', 'OD2C1A'): ((502.08000000000004, 0.0),),
('OD2C1A', 'ND2A1', 'CD31C', 'CD2O1A'): ((502.08000000000004, 0.0),),
('CD2O1A', 'CD31A', 'ND2A2', 'OD2C1A'): ((502.08000000000004, 0.0),),
('OD2C1A', 'ND2A2', 'CD31A', 'CD2O1A'): ((502.08000000000004, 0.0),),
('CD2O1A', 'CD32A', 'ND3A3', 'OD2C1A'): ((502.08000000000004, 0.0),),
('OD2C1A', 'ND3A3', 'CD32A', 'CD2O1A'): ((502.08000000000004, 0.0),),
('CD2O1A', 'CD33C', 'ND3A3', 'OD2C1A'): ((502.08000000000004, 0.0),),
('OD2C1A', 'ND3A3', 'CD33C', 'CD2O1A'): ((502.08000000000004, 0.0),),
('OD2C2A', 'CD31A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'CD31A', 'OD2C2A'): ((297.064, 0.0),),
('OD2C2A', 'CD32A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'CD32A', 'OD2C2A'): ((297.064, 0.0),),
('OD2C2A', 'CD33A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'CD33A', 'OD2C2A'): ((297.064, 0.0),),
('OD2C2A', 'CD31C', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'CD31C', 'OD2C2A'): ((297.064, 0.0),),
('OD2C2A', 'CD32C', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'CD32C', 'OD2C2A'): ((297.064, 0.0),),
('OD2C3A', 'CD31C', 'OD31F', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD31F', 'CD31C', 'OD2C3A'): ((355.64, 0.0),),
('OD2C3A', 'CD31A', 'OD31F', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD31F', 'CD31A', 'OD2C3A'): ((355.64, 0.0),),
('CD2O1A', 'CD32C', 'ND2A1', 'OD2C1A'): ((376.56, 0.0),),
('OD2C1A', 'ND2A1', 'CD32C', 'CD2O1A'): ((376.56, 0.0),),
('CD2O1A', 'CD31C', 'ND2A2', 'OD2C1A'): ((155.64480000000003, 0.0),),
('OD2C1A', 'ND2A2', 'CD31C', 'CD2O1A'): ((155.64480000000003, 0.0),),
('CD2O1A', 'CD32C', 'ND2A2', 'OD2C1A'): ((418.40000000000003, 0.0),),
('OD2C1A', 'ND2A2', 'CD32C', 'CD2O1A'): ((418.40000000000003, 0.0),),
('CD2O1A', 'CD33C', 'ND2A2', 'OD2C1A'): ((374.04960000000005, 0.0),),
('OD2C1A', 'ND2A2', 'CD33C', 'CD2O1A'): ((374.04960000000005, 0.0),),
('OD2C1A', 'ND2A1', 'CD33C', 'CD2O1A'): ((376.56, 0.0),),
('CD2O1A', 'CD33C', 'ND2A1', 'OD2C1A'): ((376.56, 0.0),),
('ND2A1', 'HDP1A', 'HDP1A', 'CD2O1A'): ((16.736, 0.0),),
('CD2O1A', 'HDP1A', 'HDP1A', 'ND2A1'): ((16.736, 0.0),),
('OD2C1A', 'ND2A3', 'CD33C', 'CD2O1A'): ((251.04000000000002, 0.0),),
('CD2O1A', 'CD33C', 'ND2A3', 'OD2C1A'): ((251.04000000000002, 0.0),),
('ND2A2', 'CD2O1A', 'CD31C', 'HDP1A'): ((128.4488, 0.0),),
('HDP1A', 'CD31C', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),),
('ND2A2', 'CD2O1A', 'CD32C', 'HDP1A'): ((167.36, 0.0),),
('HDP1A', 'CD32C', 'CD2O1A', 'ND2A2'): ((167.36, 0.0),),
('ND2A2', 'CD2O1A', 'CD33C', 'HDP1A'): ((148.9504, 0.0),),
('HDP1A', 'CD33C', 'CD2O1A', 'ND2A2'): ((148.9504, 0.0),),
('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD33A'): ((297.064, 0.0),),
('CD33A', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD32A'): ((297.064, 0.0),),
('CD32A', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD32C'): ((297.064, 0.0),),
('CD32C', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD31A'): ((297.064, 0.0),),
('CD31A', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD31C'): ((297.064, 0.0),),
('CD31C', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('ND2R5A', 'CD2R5A', 'CD2R5B', 'HDP1A'): ((1.8828, 0.0),),
('HDP1A', 'CD2R5B', 'CD2R5A', 'ND2R5A'): ((1.8828, 0.0),),
('ND2R5A', 'CD2R5B', 'CD2R5A', 'HDP1A'): ((1.8828, 0.0),),
('HDP1A', 'CD2R5A', 'CD2R5B', 'ND2R5A'): ((1.8828, 0.0),),
('CD2R5A', 'CD2R5A', 'ND2R5B', 'HDR5A'): ((2.092, 0.0),),
('HDR5A', 'ND2R5B', 'CD2R5A', 'CD2R5A'): ((2.092, 0.0),),
('CD2R5A', 'ND2R5B', 'CD2R5A', 'HDR5A'): ((2.092, 0.0),),
('HDR5A', 'CD2R5A', 'ND2R5B', 'CD2R5A'): ((2.092, 0.0),),
('CD2R5B', 'ND2R5A', 'ND2R5B', 'HDR5B'): ((2.092, 0.0),),
('HDR5B', 'ND2R5B', 'ND2R5A', 'CD2R5B'): ((2.092, 0.0),),
('CD2R5B', 'ND2R5B', 'ND2R5A', 'HDR5B'): ((2.092, 0.0),),
('HDR5B', 'ND2R5A', 'ND2R5B', 'CD2R5B'): ((2.092, 0.0),),
('CD2R5A', 'CD2R5A', 'ND2R5A', 'HDR5A'): ((2.092, 0.0),),
('HDR5A', 'ND2R5A', 'CD2R5A', 'CD2R5A'): ((2.092, 0.0),),
('CD2R5A', 'ND2R5A', 'CD2R5A', 'HDR5A'): ((2.092, 0.0),),
('HDR5A', 'CD2R5A', 'ND2R5A', 'CD2R5A'): ((2.092, 0.0),),
('ND2R5C', 'CD2R5E', 'CD2R5D', 'HDP1A'): ((1.8828, 0.0),),
('HDP1A', 'CD2R5D', 'CD2R5E', 'ND2R5C'): ((1.8828, 0.0),),
('CD2R5D', 'CD2R5D', 'ND2R5C', 'HDR5D'): ((2.092, 0.0),),
('HDR5D', 'ND2R5C', 'CD2R5D', 'CD2R5D'): ((2.092, 0.0),),
('CD2R5E', 'ND2R5C', 'ND2R5C', 'HDR5E'): ((2.092, 0.0),),
('HDR5E', 'ND2R5C', 'ND2R5C', 'CD2R5E'): ((2.092, 0.0),),
('CD2N1A', 'ND2P1A', 'ND2P1A', 'ND2P1A'): ((167.36, 0.0),),
('ND2P1A', 'ND2P1A', 'ND2P1A', 'CD2N1A'): ((167.36, 0.0),),
('HDR5A', 'ND2R5A', 'CD2R5C', 'CD2R5A'): ((1.8828, 0.0),),
('CD2R5A', 'CD2R5C', 'ND2R5A', 'HDR5A'): ((1.8828, 0.0),),
('HDR5A', 'CD2R5C', 'ND2R5A', 'CD2R5A'): ((1.8828, 0.0),),
('CD2R5A', 'ND2R5A', 'CD2R5C', 'HDR5A'): ((1.8828, 0.0),),
('HDP1A', 'CD2R5A', 'CD2R5A', 'ND2R5A'): ((1.8828, 0.0),),
('ND2R5A', 'CD2R5A', 'CD2R5A', 'HDP1A'): ((1.8828, 0.0),),
('HDR5C', 'CD2R5A', 'CD2R5C', 'CD2R5C'): ((1.8828, 0.0),),
('CD2R5C', 'CD2R5C', 'CD2R5A', 'HDR5C'): ((1.8828, 0.0),),
('HDR5C', 'CD2R5C', 'CD2R5A', 'CD2R5C'): ((1.8828, 0.0),),
('CD2R5C', 'CD2R5A', 'CD2R5C', 'HDR5C'): ((1.8828, 0.0),),
('HDP1A', 'CD2R5A', 'CD2R6D', 'ND2R5A'): ((1.8828, 0.0),),
('ND2R5A', 'CD2R6D', 'CD2R5A', 'HDP1A'): ((1.8828, 0.0),),
('HDP1A', 'CD2R6D', 'CD2R5A', 'ND2R5A'): ((1.8828, 0.0),),
('ND2R5A', 'CD2R5A', 'CD2R6D', 'HDP1A'): ((1.8828, 0.0),),
('CD2R6A', 'CD2R6A', 'CD2R6D', 'HDR6A'): ((1.8828, 0.0),),
('HDR6A', 'CD2R6D', 'CD2R6A', 'CD2R6A'): ((1.8828, 0.0),),
('HDR6A', 'CD2R6A', 'CD2R6D', 'CD2R6A'): ((1.8828, 0.0),),
('CD2R6A', 'CD2R6D', 'CD2R6A', 'HDR6A'): ((1.8828, 0.0),),
('HDR5C', 'CD2R6D', 'CD2R5A', 'CD2R5C'): ((1.8828, 0.0),),
('CD2R5C', 'CD2R5A', 'CD2R6D', 'HDR5C'): ((1.8828, 0.0),),
('HDR5C', 'CD2R5A', 'CD2R6D', 'CD2R5C'): ((1.8828, 0.0),),
('CD2R5C', 'CD2R6D', 'CD2R5A', 'HDR5C'): ((1.8828, 0.0),),
('ND2R5A', 'CD2R6F', 'CD2R5B', 'HDP1A'): ((1.8828, 0.0),),
('HDP1A', 'CD2R5B', 'CD2R6F', 'ND2R5A'): ((1.8828, 0.0),),
('ND2R5A', 'CD2R5B', 'CD2R6F', 'HDP1A'): ((1.8828, 0.0),),
('HDP1A', 'CD2R6F', 'CD2R5B', 'ND2R5A'): ((1.8828, 0.0),),
('CD2R6F', 'CD2R6F', 'CD2R6B', 'ND2R5A'): ((83.68, 0.0),),
('ND2R5A', 'CD2R6B', 'CD2R6F', 'CD2R6F'): ((83.68, 0.0),),
('CD2R6F', 'CD2R6B', 'CD2R6F', 'ND2R5A'): ((83.68, 0.0),),
('ND2R5A', 'CD2R6F', 'CD2R6B', 'CD2R6F'): ((83.68, 0.0),),
('CD2R6F', 'CD2R6F', 'ND2R6B', 'ND2R5B'): ((41.84, 0.0),),
('ND2R5B', 'ND2R6B', 'CD2R6F', 'CD2R6F'): ((41.84, 0.0),),
('CD2R6F', 'ND2R6B', 'CD2R6F', 'ND2R5B'): ((41.84, 0.0),),
('ND2R5B', 'CD2R6F', 'ND2R6B', 'CD2R6F'): ((41.84, 0.0),),
('CD2R6F', 'CD2R6F', 'CD2R6B', 'ND2R5B'): ((83.68, 0.0),),
('ND2R5B', 'CD2R6B', 'CD2R6F', 'CD2R6F'): ((83.68, 0.0),),
('CD2R6F', 'CD2R6B', 'CD2R6F', 'ND2R5B'): ((83.68, 0.0),),
('ND2R5B', 'CD2R6F', 'CD2R6B', 'CD2R6F'): ((83.68, 0.0),),
('CD2R6F', 'CD2R6F', 'ND2R6B', 'ND2R5A'): ((41.84, 0.0),),
('ND2R5A', 'ND2R6B', 'CD2R6F', 'CD2R6F'): ((41.84, 0.0),),
('CD2R6F', 'ND2R6B', 'CD2R6F', 'ND2R5A'): ((41.84, 0.0),),
('ND2R5A', 'CD2R6F', 'ND2R6B', 'CD2R6F'): ((41.84, 0.0),),
('CD2O4A', 'ND2R6B', 'ND2R6B', 'OD2C1B'): ((334.72, 0.0),),
('OD2C1B', 'ND2R6B', 'ND2R6B', 'CD2O4A'): ((334.72, 0.0),),
('CD2O4A', 'ND2R6C', 'ND2R6C', 'OD2C1B'): ((334.72, 0.0),),
('OD2C1B', 'ND2R6C', 'ND2R6C', 'CD2O4A'): ((334.72, 0.0),),
('CD2O4A', 'ND2R6C', 'ND2R6B', 'OD2C1B'): ((334.72, 0.0),),
('OD2C1B', 'ND2R6B', 'ND2R6C', 'CD2O4A'): ((334.72, 0.0),),
('CD2R6B', 'ND2R6B', 'CD2R6J', 'ND2B1'): ((251.04000000000002, 0.0),),
('ND2B1', 'CD2R6J', 'ND2R6B', 'CD2R6B'): ((251.04000000000002, 0.0),),
('ND2R6B', 'CD2R6H', 'CD2O4A', 'HDP1A'): ((4.184, 0.0),),
('HDP1A', 'CD2O4A', 'CD2R6H', 'ND2R6B'): ((4.184, 0.0),),
('ND2R6C', 'CD2R6H', 'CD2O4A', 'HDP1A'): ((4.184, 0.0),),
('HDP1A', 'CD2O4A', 'CD2R6H', 'ND2R6C'): ((4.184, 0.0),),
('ND2R6C', 'CD2R6H', 'CD2O4A', 'CD33A'): ((58.576, 0.0),),
('CD33A', 'CD2O4A', 'CD2R6H', 'ND2R6C'): ((58.576, 0.0),),
('CD2O4A', 'ND2R6B', 'ND2R6C', 'OD2C1B'): ((460.24, 0.0),),
('OD2C1B', 'ND2R6C', 'ND2R6B', 'CD2O4A'): ((460.24, 0.0),),
('CD2O4A', 'ND2R6C', 'CD2R6J', 'OD2C1B'): ((376.56, 0.0),),
('OD2C1B', 'CD2R6J', 'ND2R6C', 'CD2O4A'): ((376.56, 0.0),),
('CD2R6J', 'CD2O4A', 'CD2R6H', 'CD33A'): ((58.576, 0.0),),
('CD33A', 'CD2R6H', 'CD2O4A', 'CD2R6J'): ((58.576, 0.0),),
('CD2R6C', 'ND2R6B', 'ND2R6C', 'ND2B1'): ((167.36, 0.0),),
('ND2B1', 'ND2R6C', 'ND2R6B', 'CD2R6C'): ((167.36, 0.0),),
('CD2O4A', 'ND2R6C', 'CD2R6F', 'OD2C1B'): ((376.56, 0.0),),
('OD2C1B', 'CD2R6F', 'ND2R6C', 'CD2O4A'): ((376.56, 0.0),),
('ND2B1', 'HDP1A', 'CD2R6C', 'HDP1A'): ((25.104, 0.0),),
('HDP1A', 'CD2R6C', 'HDP1A', 'ND2B1'): ((25.104, 0.0),),
('OD2C3A', 'CD33A', 'OD30C', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD30C', 'CD33A', 'OD2C3A'): ((355.64, 0.0),),
('OD2C3A', 'CD32A', 'OD30C', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD30C', 'CD32A', 'OD2C3A'): ((355.64, 0.0),),
('OD2C3A', 'CD33C', 'OD30C', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD30C', 'CD33C', 'OD2C3A'): ((355.64, 0.0),),
('OD2C3A', 'CD32C', 'OD30C', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD30C', 'CD32C', 'OD2C3A'): ((355.64, 0.0),),
('OD2C3A', 'CD31C', 'OD30C', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD30C', 'CD31C', 'OD2C3A'): ((355.64, 0.0),),
('CD2O3A', 'OD31F', 'CD33C', 'OD2C3A'): ((355.64, 0.0),),
('OD2C3A', 'CD33C', 'OD31F', 'CD2O3A'): ((355.64, 0.0),),
('CD2C1A', 'CD2C1A', 'CD32A', 'HD2C1A'): ((8.368, 0.0),),
('HD2C1A', 'CD32A', 'CD2C1A', 'CD2C1A'): ((8.368, 0.0),),
('CD2C1A', 'CD2C1B', 'CD32A', 'HD2C1A'): ((8.368, 0.0),),
('HD2C1A', 'CD32A', 'CD2C1B', 'CD2C1A'): ((8.368, 0.0),),
('CD2C1A', 'CD32A', 'CD2C1A', 'HD2C1A'): ((8.368, 0.0),),
('HD2C1A', 'CD2C1A', 'CD32A', 'CD2C1A'): ((8.368, 0.0),),
('CD2C1A', 'CD32A', 'CD2C1B', 'HD2C1A'): ((8.368, 0.0),),
('HD2C1A', 'CD2C1B', 'CD32A', 'CD2C1A'): ((8.368, 0.0),),
('CD2C1A', 'CD2C1A', 'CD33A', 'HD2C1A'): ((8.368, 0.0),),
('HD2C1A', 'CD33A', 'CD2C1A', 'CD2C1A'): ((8.368, 0.0),),
('CD2C1A', 'CD2C1B', 'CD33A', 'HD2C1A'): ((8.368, 0.0),),
('HD2C1A', 'CD33A', 'CD2C1B', 'CD2C1A'): ((8.368, 0.0),),
('CD2O1D', 'CD33C', 'CD33C', 'OD2C1D'): ((410.03200000000004, 0.0),),
('OD2C1D', 'CD33C', 'CD33C', 'CD2O1D'): ((410.03200000000004, 0.0),),
('CD2O1D', 'CD33C', 'CD32C', 'OD2C1D'): ((389.112, 0.0),),
('OD2C1D', 'CD32C', 'CD33C', 'CD2O1D'): ((389.112, 0.0),),
('CD2O1D', 'CD32C', 'CD32C', 'OD2C1D'): ((397.48, 0.0),),
('OD2C1D', 'CD32C', 'CD32C', 'CD2O1D'): ((397.48, 0.0),),
('CD2O1C', 'HDP1C', 'CD33C', 'OD2C1D'): ((313.8, 0.0),),
('OD2C1D', 'CD33C', 'HDP1C', 'CD2O1C'): ((313.8, 0.0),),
('CD2O1C', 'HDP1C', 'CD32C', 'OD2C1D'): ((298.3192, 0.0),),
('OD2C1D', 'CD32C', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),),
('CD2O1C', 'HDP1C', 'CD33C', 'OD2C1C'): ((313.8, 0.0),),
('OD2C1C', 'CD33C', 'HDP1C', 'CD2O1C'): ((313.8, 0.0),),
('CD2O1C', 'HDP1C', 'CD32C', 'OD2C1C'): ((298.3192, 0.0),),
('OD2C1C', 'CD32C', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),),
('CD2O1C', 'HDP1C', 'CD31C', 'OD2C1C'): ((298.3192, 0.0),),
('OD2C1C', 'CD31C', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),),
('CD2O1C', 'HDP1C', 'CD31G', 'OD2C1C'): ((298.3192, 0.0),),
('OD2C1C', 'CD31G', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),),
('CD2O1D', 'CD32F', 'CD31G', 'OD2C1D'): ((389.112, 0.0),),
('OD2C1D', 'CD31G', 'CD32F', 'CD2O1D'): ((389.112, 0.0),),
('CD2O1C', 'ND2A1', 'OD2C1D', 'HDP1C'): ((292.88, 0.0),),
('HDP1C', 'OD2C1D', 'ND2A1', 'CD2O1C'): ((292.88, 0.0),),
('CD2O1A', 'CD31DC', 'ND3A3', 'OD2C1A'): ((0.0, 0.0),),
('OD2C1A', 'ND3A3', 'CD31DC', 'CD2O1A'): ((0.0, 0.0),),
('ND3A3', 'CD2O1A', 'CD31DC', 'CD32A'): ((0.0, 0.0),),
('CD32A', 'CD31DC', 'CD2O1A', 'ND3A3'): ((0.0, 0.0),),
('CD2O1A', 'CD31DC', 'ND2A1', 'OD2C1A'): ((502.08000000000004, 0.0),),
('OD2C1A', 'ND2A1', 'CD31DC', 'CD2O1A'): ((502.08000000000004, 0.0),),
('OD2C2A', 'CD31DC', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'OD2C2A', 'CD31DC', 'OD2C2A'): ((297.064, 0.0),),
('OD2C3A', 'CD31DC', 'OD31F', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD31F', 'CD31DC', 'OD2C3A'): ((355.64, 0.0),),
('CD2O1A', 'CD31DC', 'ND2A2', 'OD2C1A'): ((155.64480000000003, 0.0),),
('OD2C1A', 'ND2A2', 'CD31DC', 'CD2O1A'): ((155.64480000000003, 0.0),),
('ND2A2', 'CD2O1A', 'CD31DC', 'HDP1A'): ((128.4488, 0.0),),
('HDP1A', 'CD31DC', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),),
('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD31DC'): ((297.064, 0.0),),
('CD31DC', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),),
('OD2C3A', 'CD31DC', 'OD30C', 'CD2O3A'): ((355.64, 0.0),),
('CD2O3A', 'OD30C', 'CD31DC', 'OD2C3A'): ((355.64, 0.0),),
('CD2O1C', 'HDP1C', 'CD31DC', 'OD2C1C'): ((298.3192, 0.0),),
('OD2C1C', 'CD31DC', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),),
('ND2A2', 'CD2O1A', 'CD31HB', 'HDP1A'): ((128.4488, 0.0),),
('HDP1A', 'CD31HB', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),),
('CD2O2A', 'CD31HC', 'OD2C2A', 'OD2C2A'): ((297.064, 0.0),),
('OD2C2A', 'OD2C2A', 'CD31HC', 'CD2O2A'): ((297.064, 0.0),),
('CD2O2A', 'CD30HA', 'OD2C2A', 'OD2C2A'): ((297.064, 0.0),),
('OD2C2A', 'OD2C2A', 'CD30HA', 'CD2O2A'): ((297.064, 0.0),),
('ND2A2', 'CD2O1A', 'CD31HA', 'HDP1A'): ((128.4488, 0.0),),
('HDP1A', 'CD31HA', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),),
}
   
residue_order = {'ALAD': 0, 'ALA': 1, 'ARG': 2, 'ASN': 3, 'ASP': 4, 'CYS': 5, 'GLN': 6, 'GLU': 7, 'GLY': 8, 'HSD': 9, 'HSE': 10, 'HSP': 11, 'ILE': 12, 'LEU': 13, 'LYS': 14, 'MET': 15, 'PHE': 16, 'PRO': 17, 'SER': 18, 'THR': 19, 'TRP': 20, 'TYR': 21, 'VAL': 22, 'ALDD': 23, 'DALA': 24, 'DARG': 25, 'DASN': 26, 'DASP': 27, 'DCYS': 28, 'DGLN': 29, 'DGLU': 30, 'DGLY': 31, 'DHSD': 32, 'DHSE': 33, 'DHSP': 34, 'DILE': 35, 'DLEU': 36, 'DLYS': 37, 'DMET': 38, 'DPHE': 39, 'DPRO': 40, 'DSER': 41, 'DTHR': 42, 'DTRP': 43, 'DTYR': 44, 'DVAL': 45, 'ALLO': 46, 'PSIC': 47, 'AGALA': 48, 'BGALA': 49, 'AGLCA': 50, 'BGLCA': 51, 'AIDOA': 52, 'BIDOA': 53, 'AGLCNA': 54, 'BGLCNA': 55, 'AGALNA': 56, 'BGALNA': 57, 'AMANNA': 58, 'BMANNA': 59, 'ARHMNA': 60, 'BRHMNA': 61, 'ANE5AC': 62, 'BNE5AC': 63, '2BTE': 64, '2BTD': 65, '2PTE': 66, '2PTD': 67, '2HEX': 68, '2HED': 69, '3HEX': 70, '3HED': 71, '5DEC': 72, '5DED': 73, 'AALD': 74, 'PALD': 75, 'BALD': 76, 'IBLD': 77, 'ACO': 78, 'BTON': 79, 'FORM': 80, 'ACEM': 81, 'NMA': 82, 'NEA': 83, 'NPA': 84, 'DMA': 85, 'IMID': 86, '4MIM': 87, '4MIE': 88, 'INDO': 89, 'PUR0': 90, 'PUR1': 91, 'MIND': 92, 'ACET': 93, 'GUAN': 94, 'MGUAN': 95, 'BGUAN': 96, 'IMIM': 97, 'ACEH': 98, 'MAS': 99, 'EAS': 100, 'MPRO': 101, 'MBU': 102, 'GLYC': 103, 'GLYP': 104, 'PRPC': 105, 'DMPC': 106, 'DPPC': 107, 'DSPC': 108, 'DOPC': 109, 'DLPE': 110, 'DPPE': 111, 'POPC': 112, 'DOPE': 113, 'POPE': 114, 'DLPC': 115} def extract_atom_name(raw_atom_name, templates):
patch_order = {'ACE': 0, 'ACP': 1, 'CTER': 2, 'CTEG': 3, 'CTEP': 4, 'CNEU': 5, 'CNEG': 6, 'CNES': 7, 'CT1': 8, 'CT1G': 9, 'CT2': 10, 'CT2G': 11, 'CT2S': 12, 'CT3': 13, 'LINK': 14, 'HS2': 15, 'KAC': 16, 'DACE': 17, 'DACP': 18, 'DCTER': 19, 'DCTEG': 20, 'DCTEP': 21, 'DCTES': 22, 'DCNEU': 23, 'DCNEG': 24, 'DCNES': 25, 'DCT1': 26, 'DCT1G': 27, 'DCT2': 28, 'DCT2G': 29, 'DCT2S': 30, 'DCT3': 31} # Process Drude particles.
atom_name_prefix = ""
if raw_atom_name.startswith("Drude-"):
raw_atom_name = raw_atom_name[len("Drude-"):]
atom_name_prefix = "D"
   
periodic_improper_types = {} # Return None to indicate an atom without template name information.
harmonic_improper_types = {('OD2C3A', 'CD32C', 'OD31F', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD31F', 'CD32C', 'OD2C3A'): ((355.64, 0.0),), ('CD2O1A', 'CD32A', 'ND2A2', 'OD2C1A'): ((418.40000000000003, 0.0),), ('OD2C1A', 'ND2A2', 'CD32A', 'CD2O1A'): ((418.40000000000003, 0.0),), ('CD2O1A', 'CD31C', 'ND3A3', 'OD2C1A'): ((0.0, 0.0),), ('OD2C1A', 'ND3A3', 'CD31C', 'CD2O1A'): ((0.0, 0.0),), ('CD2O1A', 'CD32C', 'ND3A3', 'OD2C1A'): ((0.0, 0.0),), ('OD2C1A', 'ND3A3', 'CD32C', 'CD2O1A'): ((0.0, 0.0),), ('ND3A3', 'CD2O1A', 'CD31C', 'CD32A'): ((0.0, 0.0),), ('CD32A', 'CD31C', 'CD2O1A', 'ND3A3'): ((0.0, 0.0),), ('CD2O1A', 'CD31C', 'ND2A1', 'OD2C1A'): ((502.08000000000004, 0.0),), ('OD2C1A', 'ND2A1', 'CD31C', 'CD2O1A'): ((502.08000000000004, 0.0),), ('CD2O1A', 'CD31A', 'ND2A2', 'OD2C1A'): ((502.08000000000004, 0.0),), ('OD2C1A', 'ND2A2', 'CD31A', 'CD2O1A'): ((502.08000000000004, 0.0),), ('CD2O1A', 'CD32A', 'ND3A3', 'OD2C1A'): ((502.08000000000004, 0.0),), ('OD2C1A', 'ND3A3', 'CD32A', 'CD2O1A'): ((502.08000000000004, 0.0),), ('CD2O1A', 'CD33C', 'ND3A3', 'OD2C1A'): ((502.08000000000004, 0.0),), ('OD2C1A', 'ND3A3', 'CD33C', 'CD2O1A'): ((502.08000000000004, 0.0),), ('OD2C2A', 'CD31A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'CD31A', 'OD2C2A'): ((297.064, 0.0),), ('OD2C2A', 'CD32A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'CD32A', 'OD2C2A'): ((297.064, 0.0),), ('OD2C2A', 'CD33A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'CD33A', 'OD2C2A'): ((297.064, 0.0),), ('OD2C2A', 'CD31C', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'CD31C', 'OD2C2A'): ((297.064, 0.0),), ('OD2C2A', 'CD32C', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'CD32C', 'OD2C2A'): ((297.064, 0.0),), ('OD2C3A', 'CD31C', 'OD31F', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD31F', 'CD31C', 'OD2C3A'): ((355.64, 0.0),), ('OD2C3A', 'CD31A', 'OD31F', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD31F', 'CD31A', 'OD2C3A'): ((355.64, 0.0),), ('CD2O1A', 'CD32C', 'ND2A1', 'OD2C1A'): ((376.56, 0.0),), ('OD2C1A', 'ND2A1', 'CD32C', 'CD2O1A'): ((376.56, 0.0),), ('CD2O1A', 'CD31C', 'ND2A2', 'OD2C1A'): ((155.64480000000003, 0.0),), ('OD2C1A', 'ND2A2', 'CD31C', 'CD2O1A'): ((155.64480000000003, 0.0),), ('CD2O1A', 'CD32C', 'ND2A2', 'OD2C1A'): ((418.40000000000003, 0.0),), ('OD2C1A', 'ND2A2', 'CD32C', 'CD2O1A'): ((418.40000000000003, 0.0),), ('CD2O1A', 'CD33C', 'ND2A2', 'OD2C1A'): ((374.04960000000005, 0.0),), ('OD2C1A', 'ND2A2', 'CD33C', 'CD2O1A'): ((374.04960000000005, 0.0),), ('OD2C1A', 'ND2A1', 'CD33C', 'CD2O1A'): ((376.56, 0.0),), ('CD2O1A', 'CD33C', 'ND2A1', 'OD2C1A'): ((376.56, 0.0),), ('ND2A1', 'HDP1A', 'HDP1A', 'CD2O1A'): ((16.736, 0.0),), ('CD2O1A', 'HDP1A', 'HDP1A', 'ND2A1'): ((16.736, 0.0),), ('OD2C1A', 'ND2A3', 'CD33C', 'CD2O1A'): ((251.04000000000002, 0.0),), ('CD2O1A', 'CD33C', 'ND2A3', 'OD2C1A'): ((251.04000000000002, 0.0),), ('ND2A2', 'CD2O1A', 'CD31C', 'HDP1A'): ((128.4488, 0.0),), ('HDP1A', 'CD31C', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),), ('ND2A2', 'CD2O1A', 'CD32C', 'HDP1A'): ((167.36, 0.0),), ('HDP1A', 'CD32C', 'CD2O1A', 'ND2A2'): ((167.36, 0.0),), ('ND2A2', 'CD2O1A', 'CD33C', 'HDP1A'): ((148.9504, 0.0),), ('HDP1A', 'CD33C', 'CD2O1A', 'ND2A2'): ((148.9504, 0.0),), ('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD33A'): ((297.064, 0.0),), ('CD33A', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD32A'): ((297.064, 0.0),), ('CD32A', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD32C'): ((297.064, 0.0),), ('CD32C', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD31A'): ((297.064, 0.0),), ('CD31A', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD31C'): ((297.064, 0.0),), ('CD31C', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('ND2R5A', 'CD2R5A', 'CD2R5B', 'HDP1A'): ((1.8828, 0.0),), ('HDP1A', 'CD2R5B', 'CD2R5A', 'ND2R5A'): ((1.8828, 0.0),), ('ND2R5A', 'CD2R5B', 'CD2R5A', 'HDP1A'): ((1.8828, 0.0),), ('HDP1A', 'CD2R5A', 'CD2R5B', 'ND2R5A'): ((1.8828, 0.0),), ('CD2R5A', 'CD2R5A', 'ND2R5B', 'HDR5A'): ((2.092, 0.0),), ('HDR5A', 'ND2R5B', 'CD2R5A', 'CD2R5A'): ((2.092, 0.0),), ('CD2R5A', 'ND2R5B', 'CD2R5A', 'HDR5A'): ((2.092, 0.0),), ('HDR5A', 'CD2R5A', 'ND2R5B', 'CD2R5A'): ((2.092, 0.0),), ('CD2R5B', 'ND2R5A', 'ND2R5B', 'HDR5B'): ((2.092, 0.0),), ('HDR5B', 'ND2R5B', 'ND2R5A', 'CD2R5B'): ((2.092, 0.0),), ('CD2R5B', 'ND2R5B', 'ND2R5A', 'HDR5B'): ((2.092, 0.0),), ('HDR5B', 'ND2R5A', 'ND2R5B', 'CD2R5B'): ((2.092, 0.0),), ('CD2R5A', 'CD2R5A', 'ND2R5A', 'HDR5A'): ((2.092, 0.0),), ('HDR5A', 'ND2R5A', 'CD2R5A', 'CD2R5A'): ((2.092, 0.0),), ('CD2R5A', 'ND2R5A', 'CD2R5A', 'HDR5A'): ((2.092, 0.0),), ('HDR5A', 'CD2R5A', 'ND2R5A', 'CD2R5A'): ((2.092, 0.0),), ('ND2R5C', 'CD2R5E', 'CD2R5D', 'HDP1A'): ((1.8828, 0.0),), ('HDP1A', 'CD2R5D', 'CD2R5E', 'ND2R5C'): ((1.8828, 0.0),), ('CD2R5D', 'CD2R5D', 'ND2R5C', 'HDR5D'): ((2.092, 0.0),), ('HDR5D', 'ND2R5C', 'CD2R5D', 'CD2R5D'): ((2.092, 0.0),), ('CD2R5E', 'ND2R5C', 'ND2R5C', 'HDR5E'): ((2.092, 0.0),), ('HDR5E', 'ND2R5C', 'ND2R5C', 'CD2R5E'): ((2.092, 0.0),), ('CD2N1A', 'ND2P1A', 'ND2P1A', 'ND2P1A'): ((167.36, 0.0),), ('ND2P1A', 'ND2P1A', 'ND2P1A', 'CD2N1A'): ((167.36, 0.0),), ('HDR5A', 'ND2R5A', 'CD2R5C', 'CD2R5A'): ((1.8828, 0.0),), ('CD2R5A', 'CD2R5C', 'ND2R5A', 'HDR5A'): ((1.8828, 0.0),), ('HDR5A', 'CD2R5C', 'ND2R5A', 'CD2R5A'): ((1.8828, 0.0),), ('CD2R5A', 'ND2R5A', 'CD2R5C', 'HDR5A'): ((1.8828, 0.0),), ('HDP1A', 'CD2R5A', 'CD2R5A', 'ND2R5A'): ((1.8828, 0.0),), ('ND2R5A', 'CD2R5A', 'CD2R5A', 'HDP1A'): ((1.8828, 0.0),), ('HDR5C', 'CD2R5A', 'CD2R5C', 'CD2R5C'): ((1.8828, 0.0),), ('CD2R5C', 'CD2R5C', 'CD2R5A', 'HDR5C'): ((1.8828, 0.0),), ('HDR5C', 'CD2R5C', 'CD2R5A', 'CD2R5C'): ((1.8828, 0.0),), ('CD2R5C', 'CD2R5A', 'CD2R5C', 'HDR5C'): ((1.8828, 0.0),), ('HDP1A', 'CD2R5A', 'CD2R6D', 'ND2R5A'): ((1.8828, 0.0),), ('ND2R5A', 'CD2R6D', 'CD2R5A', 'HDP1A'): ((1.8828, 0.0),), ('HDP1A', 'CD2R6D', 'CD2R5A', 'ND2R5A'): ((1.8828, 0.0),), ('ND2R5A', 'CD2R5A', 'CD2R6D', 'HDP1A'): ((1.8828, 0.0),), ('CD2R6A', 'CD2R6A', 'CD2R6D', 'HDR6A'): ((1.8828, 0.0),), ('HDR6A', 'CD2R6D', 'CD2R6A', 'CD2R6A'): ((1.8828, 0.0),), ('HDR6A', 'CD2R6A', 'CD2R6D', 'CD2R6A'): ((1.8828, 0.0),), ('CD2R6A', 'CD2R6D', 'CD2R6A', 'HDR6A'): ((1.8828, 0.0),), ('HDR5C', 'CD2R6D', 'CD2R5A', 'CD2R5C'): ((1.8828, 0.0),), ('CD2R5C', 'CD2R5A', 'CD2R6D', 'HDR5C'): ((1.8828, 0.0),), ('HDR5C', 'CD2R5A', 'CD2R6D', 'CD2R5C'): ((1.8828, 0.0),), ('CD2R5C', 'CD2R6D', 'CD2R5A', 'HDR5C'): ((1.8828, 0.0),), ('ND2R5A', 'CD2R6F', 'CD2R5B', 'HDP1A'): ((1.8828, 0.0),), ('HDP1A', 'CD2R5B', 'CD2R6F', 'ND2R5A'): ((1.8828, 0.0),), ('ND2R5A', 'CD2R5B', 'CD2R6F', 'HDP1A'): ((1.8828, 0.0),), ('HDP1A', 'CD2R6F', 'CD2R5B', 'ND2R5A'): ((1.8828, 0.0),), ('CD2R6F', 'CD2R6F', 'CD2R6B', 'ND2R5A'): ((83.68, 0.0),), ('ND2R5A', 'CD2R6B', 'CD2R6F', 'CD2R6F'): ((83.68, 0.0),), ('CD2R6F', 'CD2R6B', 'CD2R6F', 'ND2R5A'): ((83.68, 0.0),), ('ND2R5A', 'CD2R6F', 'CD2R6B', 'CD2R6F'): ((83.68, 0.0),), ('CD2R6F', 'CD2R6F', 'ND2R6B', 'ND2R5B'): ((41.84, 0.0),), ('ND2R5B', 'ND2R6B', 'CD2R6F', 'CD2R6F'): ((41.84, 0.0),), ('CD2R6F', 'ND2R6B', 'CD2R6F', 'ND2R5B'): ((41.84, 0.0),), ('ND2R5B', 'CD2R6F', 'ND2R6B', 'CD2R6F'): ((41.84, 0.0),), ('CD2R6F', 'CD2R6F', 'CD2R6B', 'ND2R5B'): ((83.68, 0.0),), ('ND2R5B', 'CD2R6B', 'CD2R6F', 'CD2R6F'): ((83.68, 0.0),), ('CD2R6F', 'CD2R6B', 'CD2R6F', 'ND2R5B'): ((83.68, 0.0),), ('ND2R5B', 'CD2R6F', 'CD2R6B', 'CD2R6F'): ((83.68, 0.0),), ('CD2R6F', 'CD2R6F', 'ND2R6B', 'ND2R5A'): ((41.84, 0.0),), ('ND2R5A', 'ND2R6B', 'CD2R6F', 'CD2R6F'): ((41.84, 0.0),), ('CD2R6F', 'ND2R6B', 'CD2R6F', 'ND2R5A'): ((41.84, 0.0),), ('ND2R5A', 'CD2R6F', 'ND2R6B', 'CD2R6F'): ((41.84, 0.0),), ('CD2O4A', 'ND2R6B', 'ND2R6B', 'OD2C1B'): ((334.72, 0.0),), ('OD2C1B', 'ND2R6B', 'ND2R6B', 'CD2O4A'): ((334.72, 0.0),), ('CD2O4A', 'ND2R6C', 'ND2R6C', 'OD2C1B'): ((334.72, 0.0),), ('OD2C1B', 'ND2R6C', 'ND2R6C', 'CD2O4A'): ((334.72, 0.0),), ('CD2O4A', 'ND2R6C', 'ND2R6B', 'OD2C1B'): ((334.72, 0.0),), ('OD2C1B', 'ND2R6B', 'ND2R6C', 'CD2O4A'): ((334.72, 0.0),), ('CD2R6B', 'ND2R6B', 'CD2R6J', 'ND2B1'): ((251.04000000000002, 0.0),), ('ND2B1', 'CD2R6J', 'ND2R6B', 'CD2R6B'): ((251.04000000000002, 0.0),), ('ND2R6B', 'CD2R6H', 'CD2O4A', 'HDP1A'): ((4.184, 0.0),), ('HDP1A', 'CD2O4A', 'CD2R6H', 'ND2R6B'): ((4.184, 0.0),), ('ND2R6C', 'CD2R6H', 'CD2O4A', 'HDP1A'): ((4.184, 0.0),), ('HDP1A', 'CD2O4A', 'CD2R6H', 'ND2R6C'): ((4.184, 0.0),), ('ND2R6C', 'CD2R6H', 'CD2O4A', 'CD33A'): ((58.576, 0.0),), ('CD33A', 'CD2O4A', 'CD2R6H', 'ND2R6C'): ((58.576, 0.0),), ('CD2O4A', 'ND2R6B', 'ND2R6C', 'OD2C1B'): ((460.24, 0.0),), ('OD2C1B', 'ND2R6C', 'ND2R6B', 'CD2O4A'): ((460.24, 0.0),), ('CD2O4A', 'ND2R6C', 'CD2R6J', 'OD2C1B'): ((376.56, 0.0),), ('OD2C1B', 'CD2R6J', 'ND2R6C', 'CD2O4A'): ((376.56, 0.0),), ('CD2R6J', 'CD2O4A', 'CD2R6H', 'CD33A'): ((58.576, 0.0),), ('CD33A', 'CD2R6H', 'CD2O4A', 'CD2R6J'): ((58.576, 0.0),), ('CD2R6C', 'ND2R6B', 'ND2R6C', 'ND2B1'): ((167.36, 0.0),), ('ND2B1', 'ND2R6C', 'ND2R6B', 'CD2R6C'): ((167.36, 0.0),), ('CD2O4A', 'ND2R6C', 'CD2R6F', 'OD2C1B'): ((376.56, 0.0),), ('OD2C1B', 'CD2R6F', 'ND2R6C', 'CD2O4A'): ((376.56, 0.0),), ('ND2B1', 'HDP1A', 'CD2R6C', 'HDP1A'): ((25.104, 0.0),), ('HDP1A', 'CD2R6C', 'HDP1A', 'ND2B1'): ((25.104, 0.0),), ('OD2C3A', 'CD33A', 'OD30C', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD30C', 'CD33A', 'OD2C3A'): ((355.64, 0.0),), ('OD2C3A', 'CD32A', 'OD30C', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD30C', 'CD32A', 'OD2C3A'): ((355.64, 0.0),), ('OD2C3A', 'CD33C', 'OD30C', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD30C', 'CD33C', 'OD2C3A'): ((355.64, 0.0),), ('OD2C3A', 'CD32C', 'OD30C', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD30C', 'CD32C', 'OD2C3A'): ((355.64, 0.0),), ('OD2C3A', 'CD31C', 'OD30C', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD30C', 'CD31C', 'OD2C3A'): ((355.64, 0.0),), ('CD2O3A', 'OD31F', 'CD33C', 'OD2C3A'): ((355.64, 0.0),), ('OD2C3A', 'CD33C', 'OD31F', 'CD2O3A'): ((355.64, 0.0),), ('CD2C1A', 'CD2C1A', 'CD32A', 'HD2C1A'): ((8.368, 0.0),), ('HD2C1A', 'CD32A', 'CD2C1A', 'CD2C1A'): ((8.368, 0.0),), ('CD2C1A', 'CD2C1B', 'CD32A', 'HD2C1A'): ((8.368, 0.0),), ('HD2C1A', 'CD32A', 'CD2C1B', 'CD2C1A'): ((8.368, 0.0),), ('CD2C1A', 'CD32A', 'CD2C1A', 'HD2C1A'): ((8.368, 0.0),), ('HD2C1A', 'CD2C1A', 'CD32A', 'CD2C1A'): ((8.368, 0.0),), ('CD2C1A', 'CD32A', 'CD2C1B', 'HD2C1A'): ((8.368, 0.0),), ('HD2C1A', 'CD2C1B', 'CD32A', 'CD2C1A'): ((8.368, 0.0),), ('CD2C1A', 'CD2C1A', 'CD33A', 'HD2C1A'): ((8.368, 0.0),), ('HD2C1A', 'CD33A', 'CD2C1A', 'CD2C1A'): ((8.368, 0.0),), ('CD2C1A', 'CD2C1B', 'CD33A', 'HD2C1A'): ((8.368, 0.0),), ('HD2C1A', 'CD33A', 'CD2C1B', 'CD2C1A'): ((8.368, 0.0),), ('CD2O1D', 'CD33C', 'CD33C', 'OD2C1D'): ((410.03200000000004, 0.0),), ('OD2C1D', 'CD33C', 'CD33C', 'CD2O1D'): ((410.03200000000004, 0.0),), ('CD2O1D', 'CD33C', 'CD32C', 'OD2C1D'): ((389.112, 0.0),), ('OD2C1D', 'CD32C', 'CD33C', 'CD2O1D'): ((389.112, 0.0),), ('CD2O1D', 'CD32C', 'CD32C', 'OD2C1D'): ((397.48, 0.0),), ('OD2C1D', 'CD32C', 'CD32C', 'CD2O1D'): ((397.48, 0.0),), ('CD2O1C', 'HDP1C', 'CD33C', 'OD2C1D'): ((313.8, 0.0),), ('OD2C1D', 'CD33C', 'HDP1C', 'CD2O1C'): ((313.8, 0.0),), ('CD2O1C', 'HDP1C', 'CD32C', 'OD2C1D'): ((298.3192, 0.0),), ('OD2C1D', 'CD32C', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),), ('CD2O1C', 'HDP1C', 'CD33C', 'OD2C1C'): ((313.8, 0.0),), ('OD2C1C', 'CD33C', 'HDP1C', 'CD2O1C'): ((313.8, 0.0),), ('CD2O1C', 'HDP1C', 'CD32C', 'OD2C1C'): ((298.3192, 0.0),), ('OD2C1C', 'CD32C', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),), ('CD2O1C', 'HDP1C', 'CD31C', 'OD2C1C'): ((298.3192, 0.0),), ('OD2C1C', 'CD31C', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),), ('CD2O1C', 'HDP1C', 'CD31G', 'OD2C1C'): ((298.3192, 0.0),), ('OD2C1C', 'CD31G', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),), ('CD2O1D', 'CD32F', 'CD31G', 'OD2C1D'): ((389.112, 0.0),), ('OD2C1D', 'CD31G', 'CD32F', 'CD2O1D'): ((389.112, 0.0),), ('CD2O1C', 'ND2A1', 'OD2C1D', 'HDP1C'): ((292.88, 0.0),), ('HDP1C', 'OD2C1D', 'ND2A1', 'CD2O1C'): ((292.88, 0.0),), ('CD2O1A', 'CD31DC', 'ND3A3', 'OD2C1A'): ((0.0, 0.0),), ('OD2C1A', 'ND3A3', 'CD31DC', 'CD2O1A'): ((0.0, 0.0),), ('ND3A3', 'CD2O1A', 'CD31DC', 'CD32A'): ((0.0, 0.0),), ('CD32A', 'CD31DC', 'CD2O1A', 'ND3A3'): ((0.0, 0.0),), ('CD2O1A', 'CD31DC', 'ND2A1', 'OD2C1A'): ((502.08000000000004, 0.0),), ('OD2C1A', 'ND2A1', 'CD31DC', 'CD2O1A'): ((502.08000000000004, 0.0),), ('OD2C2A', 'CD31DC', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'OD2C2A', 'CD31DC', 'OD2C2A'): ((297.064, 0.0),), ('OD2C3A', 'CD31DC', 'OD31F', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD31F', 'CD31DC', 'OD2C3A'): ((355.64, 0.0),), ('CD2O1A', 'CD31DC', 'ND2A2', 'OD2C1A'): ((155.64480000000003, 0.0),), ('OD2C1A', 'ND2A2', 'CD31DC', 'CD2O1A'): ((155.64480000000003, 0.0),), ('ND2A2', 'CD2O1A', 'CD31DC', 'HDP1A'): ((128.4488, 0.0),), ('HDP1A', 'CD31DC', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),), ('CD2O2A', 'OD2C2A', 'OD2C2A', 'CD31DC'): ((297.064, 0.0),), ('CD31DC', 'OD2C2A', 'OD2C2A', 'CD2O2A'): ((297.064, 0.0),), ('OD2C3A', 'CD31DC', 'OD30C', 'CD2O3A'): ((355.64, 0.0),), ('CD2O3A', 'OD30C', 'CD31DC', 'OD2C3A'): ((355.64, 0.0),), ('CD2O1C', 'HDP1C', 'CD31DC', 'OD2C1C'): ((298.3192, 0.0),), ('OD2C1C', 'CD31DC', 'HDP1C', 'CD2O1C'): ((298.3192, 0.0),), ('ND2A2', 'CD2O1A', 'CD31HB', 'HDP1A'): ((128.4488, 0.0),), ('HDP1A', 'CD31HB', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),), ('CD2O2A', 'CD31HC', 'OD2C2A', 'OD2C2A'): ((297.064, 0.0),), ('OD2C2A', 'OD2C2A', 'CD31HC', 'CD2O2A'): ((297.064, 0.0),), ('CD2O2A', 'CD30HA', 'OD2C2A', 'OD2C2A'): ((297.064, 0.0),), ('OD2C2A', 'OD2C2A', 'CD30HA', 'CD2O2A'): ((297.064, 0.0),), ('ND2A2', 'CD2O1A', 'CD31HA', 'HDP1A'): ((128.4488, 0.0),), ('HDP1A', 'CD31HA', 'CD2O1A', 'ND2A2'): ((128.4488, 0.0),)} atom_name_parts = raw_atom_name.rsplit("-", maxsplit=1)
if len(atom_name_parts) &lt; 2:
return None
templates.add(atom_name_parts[0])
return f"{atom_name_prefix}{atom_name_parts[1]}"
   
def is_valid_improper(atom_indices): def is_valid_improper(atom_indices):
index_1, index_2, index_3, index_4 = atom_indices index_1, index_2, index_3, index_4 = atom_indices
...@@ -30542,23 +30887,38 @@ def find_improper(improper_types, atom_classes): ...@@ -30542,23 +30887,38 @@ def find_improper(improper_types, atom_classes):
   
residue_data = [] residue_data = []
   
for residue in topology.residues(): for residue_index, residue in enumerate(topology.residues()):
# Extract the residue or patch names and atom names from the atom type names. # Extract the residue or patch names and atom names.
templates = [] template_data = templateForResidue[residue_index]
templates = set()
if template_data is None:
# Multi-residue patch; fall back to parsing atom names because OpenMM
# leaves None in templateForResidue in this case.
atom_names = [] atom_names = []
skip_residue = False
for atom in residue.atoms(): for atom in residue.atoms():
raw_atom_name = data.atomType[atom] atom_name = extract_atom_name(data.atomType[atom], templates)
atom_is_drude = raw_atom_name.startswith("Drude-") if atom_name is None:
if atom_is_drude: # Skip residues containing atoms without template name data
atom_name_parts = raw_atom_name[len("Drude-"):].rsplit("-", maxsplit=1) # (they might be from, e.g., another solvent force field file).
atom_names.append(f"D{atom_name_parts[1]}") skip_residue = True
break
atom_names.append(atom_name)
if skip_residue:
residue_data.append(([], [], []))
continue
else: else:
atom_name_parts = raw_atom_name.rsplit("-", maxsplit=1) # Extract names from template name.
atom_names.append(atom_name_parts[1]) for template_index, template_name in enumerate(template_data.name.split("-")):
templates.append(atom_name_parts[0]) if template_index:
# Patch name.
templates.add(template_name.rsplit("_", maxsplit=1)[0])
else:
# Residue name.
templates.add(template_name)
atom_names = [template_data.atoms[data.atomTemplateIndexes[atom]].name for atom in residue.atoms()]
   
# Get all unique residue or patch names that have impropers. # Get all unique residue or patch names that have impropers.
templates = set(templates)
residue_templates = sorted( residue_templates = sorted(
(template for template in templates if template in residue_impropers), key=residue_order.get (template for template in templates if template in residue_impropers), key=residue_order.get
) )
...@@ -30661,32 +31021,548 @@ if harmonic_impropers: ...@@ -30661,32 +31021,548 @@ if harmonic_impropers:
sys.addForce(harmonic_force)</Script> sys.addForce(harmonic_force)</Script>
<Script>import openmm <Script>import openmm
   
residue_anisotropies = {'ALAD': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'ALA': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'ARG': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'ASN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LPDA', 'LPDB', 0.88, 1.32)}, 'ASP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LP1A', 'LP1B', 0.7229, 1.265), 'OD2': ('CG', 'LP2A', 'LP2B', 0.7229, 1.265)}, 'CYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SG': ('CB', 'LPGA', 'LPGB', 0.88, 1.32)}, 'GLN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LPEA', 'LPEB', 0.82322, 1.14332)}, 'GLU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LP1A', 'LP1B', 0.7229, 1.265), 'OE2': ('CD', 'LP2A', 'LP2B', 0.7229, 1.265)}, 'GLY': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'HSD': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'NE2': ('LPE2', 'CE1', 'CD2', 0.808, 1.384)}, 'HSE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'ND1': ('LPD1', 'CE1', 'CG', 0.808, 1.384)}, 'HSP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'ILE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'LEU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'LYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'MET': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SD': ('CE', 'LP1A', 'LP1B', 0.7808, 1.3662)}, 'PHE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'PRO': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'SER': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)}, 'THR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG1': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)}, 'TRP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'TYR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OH': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'VAL': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'ALDD': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DALA': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DARG': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DASN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LPDA', 'LPDB', 0.88, 1.32)}, 'DASP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LP1A', 'LP1B', 0.7229, 1.265), 'OD2': ('CG', 'LP2A', 'LP2B', 0.7229, 1.265)}, 'DCYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SG': ('CB', 'LPGA', 'LPGB', 0.88, 1.32)}, 'DGLN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LPEA', 'LPEB', 0.82322, 1.14332)}, 'DGLU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LP1A', 'LP1B', 0.7229, 1.265), 'OE2': ('CD', 'LP2A', 'LP2B', 0.7229, 1.265)}, 'DGLY': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DHSD': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'NE2': ('LPE2', 'CE1', 'CD2', 0.808, 1.384)}, 'DHSE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'ND1': ('LPD1', 'CE1', 'CG', 0.808, 1.384)}, 'DHSP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DILE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DLEU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DLYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DMET': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SD': ('CE', 'LP1A', 'LP1B', 0.7808, 1.3662)}, 'DPHE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DPRO': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DSER': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)}, 'DTHR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG1': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)}, 'DTRP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'DTYR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OH': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'DVAL': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)}, 'ALLO': {'O1': ('C1', 'LP1A', 'LP1B', 0.85956, 1.13122), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'PSIC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8665, 1.07246), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'EGLY': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)}, 'MGLYOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162)}, 'MERYOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162)}, 'DTHROL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162)}, 'LTHROL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162)}, 'MRIBOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'DARAOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'LARAOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'MXYLOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'MALLOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'DALTOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'LALTOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'DGLUOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'LGLUOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'DMANOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'LMANOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'DGULOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'LGULOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'DIDIOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'LIDIOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'MGALOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AGLC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BGLC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AALT': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BALT': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AALL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BALL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AGAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BGAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AGUL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BGUL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AIDO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BIDO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AMAN': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BMAN': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'ATAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BTAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'ARIB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'BRIB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'AARB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'BARB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'AXYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'BXYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'ALYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'BLYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'ADEO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'BDEO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)}, 'AFRU': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'BFRU': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)}, 'AGALA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'BGALA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'AGLCA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'BGLCA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'AIDOA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'BIDOA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'AGLCNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'BGLCNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'AGALNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'BGALNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'AMANNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'BMANNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'AXYL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'BXYL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'AFUC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'BFUC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'ARHM': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'BRHM': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'AQUI': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'BQUI': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'ARHMNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'BRHMNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'ANE5AC': {'O11': ('C1', 'LPT1', 'LPT2', 0.7229, 1.265), 'O12': ('C1', 'LPT3', 'LPT4', 0.7229, 1.265), 'O6': ('LPX6', 'LP6A', 'LP6B', 0.8889, 1.2222), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O7': ('C7', 'LP7A', 'LP7B', 0.8108, 1.2162), 'O8': ('C8', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O9': ('C9', 'LP9A', 'LP9B', 0.8108, 1.2162)}, 'BNE5AC': {'O11': ('C1', 'LPT1', 'LPT2', 0.7229, 1.265), 'O12': ('C1', 'LPT3', 'LPT4', 0.7229, 1.265), 'O6': ('LPX6', 'LP6A', 'LP6B', 0.8889, 1.2222), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O7': ('C7', 'LP7A', 'LP7B', 0.8108, 1.2162), 'O8': ('C8', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O9': ('C9', 'LP9A', 'LP9B', 0.8108, 1.2162)}, 'AALD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)}, 'PALD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)}, 'BALD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)}, 'IBLD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)}, 'ACO': {'O1': ('C1', 'LPA', 'LPB', 0.8665, 1.07246)}, 'BTON': {'O1': ('C1', 'LPA', 'LPB', 0.8665, 1.07246)}, 'FORM': {'O': ('C', 'LPA', 'LPB', 0.819, 1.183), 'N': ('C', 'HC', 'HT', 0.796, 1.109)}, 'ACEM': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)}, 'NMA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)}, 'NEA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)}, 'NPA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)}, 'DMA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)}, 'THF': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222)}, 'TF2M': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222)}, 'THP': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222)}, 'DIOX': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222), 'O3': ('LPX2', 'LP2A', 'LP2B', 0.8889, 1.2222)}, 'DMEE': {'O2': ('LPX', 'LP2A', 'LP2B', 0.8889, 1.2222)}, 'MEET': {'O3': ('LPX', 'LP3A', 'LP3B', 0.8889, 1.2222)}, 'DEET': {'O3': ('LPX', 'LP3A', 'LP3B', 0.8889, 1.2222)}, 'DME': {'O2': ('LPX2', 'LP2A', 'LP2B', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'MPET': {'O2': ('LPX', 'LP2A', 'LP2B', 0.8889, 1.2222)}, 'MBET': {'O2': ('LPX', 'LP2A', 'LP2B', 0.8889, 1.2222)}, 'EPET': {'O3': ('LPX', 'LP3A', 'LP3B', 0.8889, 1.2222)}, 'MESH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)}, 'ETSH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)}, 'PRSH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)}, 'BUSH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)}, 'DMS': {'S1': ('C1', 'LP1A', 'LP1B', 0.7808, 1.3662)}, 'EMS': {'S1': ('C1', 'LP1A', 'LP1B', 0.7808, 1.3662)}, 'DMDS': {'S1': ('C1', 'LP1A', 'LP1B', 0.9208, 1.0102), 'S2': ('C2', 'LP2A', 'LP2B', 0.9208, 1.0102)}, 'PHEN': {'OH': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'CRES': {'OZ': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'PYR': {'NZ': ('LP1', 'CE1', 'CE2', 1.1611, 0.6778)}, 'PYRM': {'N1': ('LP1', 'C6', 'C2', 1.2376, 0.6648), 'N3': ('LP3', 'C4', 'C2', 1.2376, 0.6648)}, 'IMID': {'NE2': ('LP1', 'CE1', 'CD2', 0.808, 1.384)}, '4MIM': {'NE2': ('LP1', 'CE1', 'CD2', 0.808, 1.384)}, '4MIE': {'ND1': ('LP1', 'CE1', 'CG', 0.808, 1.384)}, 'PUR0': {'N1': ('LP1', 'C6', 'C2', 1.2376, 0.6648), 'N3': ('LP3', 'C4', 'C2', 1.2376, 0.6648), 'N7': ('LP7', 'C5', 'C8', 0.808, 1.384)}, 'PUR1': {'N1': ('LP1', 'C6', 'C2', 1.2376, 0.6648), 'N3': ('LP3', 'C4', 'C2', 1.2376, 0.6648), 'N7': ('LP7', 'C4', 'C8', 0.808, 1.384)}, 'MEOH': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'ETOH': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'PRO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'BUO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'PRO2': {'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)}, 'BUO2': {'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)}, 'PEO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'HXO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'PEO2': {'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)}, 'B3MO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'CPO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'ACET': {'O1': ('C2', 'LP1A', 'LP1B', 0.7229, 1.265), 'O2': ('C2', 'LP2A', 'LP2B', 0.7229, 1.265)}, 'DMP': {'O11': ('O13', 'O12', 'O14', 1.0, 0.6), 'O12': ('O14', 'O11', 'O13', 1.0, 0.6), 'O13': ('P', 'O11', 'O12', 0.6, 1.0), 'O14': ('P', 'O12', 'O11', 0.6, 1.0)}, 'MP_0': {'O2': ('P1', 'LP2A', 'LP2B', 0.76473, 1.16239), 'O3': ('P1', 'LP3A', 'LP3B', 0.76473, 1.16239)}, 'MP_1': {'O2': ('P1', 'LPA', 'LPB', 0.76473, 1.16239)}, 'HP_1': {'O1': ('P1', 'LP1A', 'LP1B', 0.76473, 1.16239), 'O2': ('P1', 'LP2A', 'LP2B', 0.76473, 1.16239)}, 'HP_2': {'O1': ('P1', 'LPA', 'LPB', 0.76473, 1.16239)}, 'ETAM': {'OH1': ('C5', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'CHOL': {'OH1': ('C5', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'ACEH': {'O2': ('C2', 'LP2A', 'LP2B', 0.6968, 1.2194), 'O1': ('C2', 'LP1A', 'LP1B', 0.8108, 1.2162)}, 'MAS': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)}, 'EAS': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)}, 'MPRO': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)}, 'MBU': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)}, 'FLUB': {'F6': ('C6', 'C1', 'C5', 0.75, 1.125)}, 'MAM1': {'N1': ('C1', 'HN1', 'HN2', 0.85, 1.05)}, 'EAM1': {'N1': ('C1', 'HN1', 'HN2', 0.85, 1.05)}, 'PAM1': {'N1': ('C1', 'HN1', 'HN2', 0.85, 1.05)}, 'PE': {'O1': ('O3', 'O2', 'O4', 1.0, 0.6), 'O2': ('O4', 'O1', 'O3', 1.0, 0.6), 'O3': ('P1', 'O1', 'O2', 0.6, 1.0), 'O4': ('P1', 'O2', 'O1', 0.6, 1.0)}, 'PC': {'O1': ('O3', 'O2', 'O4', 1.0, 0.6), 'O2': ('O4', 'O1', 'O3', 1.0, 0.6), 'O3': ('P1', 'O1', 'O2', 0.6, 1.0), 'O4': ('P1', 'O2', 'O1', 0.6, 1.0)}, 'GLYC': {'O4': ('C5', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O6': ('C5', 'LP6A', 'LP6B', 0.6968, 1.2194), 'O8': ('C9', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O10': ('C9', 'LP1A', 'LP1B', 0.6968, 1.2194)}, 'GLYP': {'O4': ('C5', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O6': ('C5', 'LP6A', 'LP6B', 0.6968, 1.2194), 'O8': ('C9', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O10': ('C9', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OP1': ('OP3', 'OP2', 'OP4', 1.0, 0.6), 'OP2': ('OP4', 'OP1', 'OP3', 1.0, 0.6), 'OP3': ('P1', 'OP1', 'OP2', 0.6, 1.0), 'OP4': ('P1', 'OP2', 'OP1', 0.6, 1.0)}, 'PRPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DMPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DPPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DSPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DOPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DLPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DPPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'POPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DOPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'POPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}, 'DLPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)}} residue_anisotropies = {
patch_anisotropies = {'ACE': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'ACP': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'NNEU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)}, 'GNNU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)}, 'CTER': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'CTEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'CTEP': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'CNEU': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'CNEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'CNES': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'CT1': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'CT1G': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'ASPP': {'OD1': ('CG', 'LPP1', 'LPP2', 0.6968, 1.2194), 'OD2': ('CG', 'LPP3', 'LPP4', 0.8108, 1.2162)}, 'GLUP': {'OE1': ('CD', 'LPP1', 'LPP2', 0.6968, 1.2194), 'OE2': ('CD', 'LPP3', 'LPP4', 0.8108, 1.2162)}, 'LSN': {'NZ': ('CE', 'HZ1', 'HZ2', 0.85, 1.05)}, 'HS2': {'ND1': ('LPD1', 'CE1', 'CG', 0.808, 1.384)}, 'KAC': {'OH': ('CH', 'LPA', 'LPB', 0.82322, 1.14332)}, 'DACE': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'DACP': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)}, 'DNNEU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)}, 'DGNNU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)}, 'DCTER': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'DCTEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'DCTEP': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'DCTES': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)}, 'DCNEU': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'DCNEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'DCNES': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'DCT1': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'DCT1G': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)}, 'OMEA': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'OMEB': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, '1AOME': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, '1BOME': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)}, 'FOMEA': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222)}, 'FOMEB': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222)}} 'ALAD': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
delete_anisotropies = {'OMEA': ['O5'], 'OMEB': ['O5'], '1AOME': ['O5'], '1BOME': ['O5'], 'FOMEA': ['O4'], 'FOMEB': ['O4']} 'ALA': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'ARG': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'ASN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LPDA', 'LPDB', 0.88, 1.32)},
'ASP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LP1A', 'LP1B', 0.7229, 1.265), 'OD2': ('CG', 'LP2A', 'LP2B', 0.7229, 1.265)},
'CYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SG': ('CB', 'LPGA', 'LPGB', 0.88, 1.32)},
'GLN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LPEA', 'LPEB', 0.82322, 1.14332)},
'GLU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LP1A', 'LP1B', 0.7229, 1.265), 'OE2': ('CD', 'LP2A', 'LP2B', 0.7229, 1.265)},
'GLY': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'HSD': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'NE2': ('LPE2', 'CE1', 'CD2', 0.808, 1.384)},
'HSE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'ND1': ('LPD1', 'CE1', 'CG', 0.808, 1.384)},
'HSP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'ILE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'LEU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'LYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'MET': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SD': ('CE', 'LP1A', 'LP1B', 0.7808, 1.3662)},
'PHE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'PRO': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'SER': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)},
'THR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG1': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)},
'TRP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'TYR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OH': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'VAL': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'ALDD': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DALA': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DARG': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DASN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LPDA', 'LPDB', 0.88, 1.32)},
'DASP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OD1': ('CG', 'LP1A', 'LP1B', 0.7229, 1.265), 'OD2': ('CG', 'LP2A', 'LP2B', 0.7229, 1.265)},
'DCYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SG': ('CB', 'LPGA', 'LPGB', 0.88, 1.32)},
'DGLN': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LPEA', 'LPEB', 0.82322, 1.14332)},
'DGLU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OE1': ('CD', 'LP1A', 'LP1B', 0.7229, 1.265), 'OE2': ('CD', 'LP2A', 'LP2B', 0.7229, 1.265)},
'DGLY': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DHSD': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'NE2': ('LPE2', 'CE1', 'CD2', 0.808, 1.384)},
'DHSE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'ND1': ('LPD1', 'CE1', 'CG', 0.808, 1.384)},
'DHSP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DILE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DLEU': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DLYS': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DMET': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'SD': ('CE', 'LP1A', 'LP1B', 0.7808, 1.3662)},
'DPHE': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DPRO': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DSER': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)},
'DTHR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OG1': ('CB', 'LPGA', 'LPGB', 0.8108, 1.2162)},
'DTRP': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'DTYR': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332), 'OH': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'DVAL': {'O': ('C', 'LPOA', 'LPOB', 0.82322, 1.14332)},
'ALLO': {'O1': ('C1', 'LP1A', 'LP1B', 0.85956, 1.13122), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'PSIC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8665, 1.07246), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'EGLY': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)},
'MGLYOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162)},
'MERYOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162)},
'DTHROL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162)},
'LTHROL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162)},
'MRIBOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'DARAOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'LARAOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'MXYLOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'MALLOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'DALTOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'LALTOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'DGLUOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'LGLUOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'DMANOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'LMANOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'DGULOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'LGULOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'DIDIOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'LIDIOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'MGALOL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AGLC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BGLC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AALT': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BALT': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AALL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BALL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AGAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BGAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AGUL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BGUL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AIDO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BIDO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AMAN': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BMAN': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'ATAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BTAL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'ARIB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'BRIB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'AARB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'BARB': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'AXYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'BXYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'ALYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'BLYF': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'ADEO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'BDEO': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222), 'O5': ('C5', 'LP5A', 'LP5B', 0.8108, 1.2162)},
'AFRU': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'BFRU': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162)},
'AGALA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)},
'BGALA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)},
'AGLCA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)},
'BGLCA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)},
'AIDOA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)},
'BIDOA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O61': ('C6', 'LPT1', 'LPT2', 0.7229, 1.265), 'O62': ('C6', 'LPT3', 'LPT4', 0.7229, 1.265)},
'AGLCNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'BGLCNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'AGALNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'BGALNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'AMANNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'BMANNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O6': ('C6', 'LP6A', 'LP6B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'AXYL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'BXYL': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'AFUC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'BFUC': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'ARHM': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'BRHM': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'AQUI': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'BQUI': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'ARHMNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'BRHMNA': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162), 'O3': ('C3', 'LP3A', 'LP3B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'ANE5AC': {'O11': ('C1', 'LPT1', 'LPT2', 0.7229, 1.265), 'O12': ('C1', 'LPT3', 'LPT4', 0.7229, 1.265), 'O6': ('LPX6', 'LP6A', 'LP6B', 0.8889, 1.2222), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O7': ('C7', 'LP7A', 'LP7B', 0.8108, 1.2162), 'O8': ('C8', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O9': ('C9', 'LP9A', 'LP9B', 0.8108, 1.2162)},
'BNE5AC': {'O11': ('C1', 'LPT1', 'LPT2', 0.7229, 1.265), 'O12': ('C1', 'LPT3', 'LPT4', 0.7229, 1.265), 'O6': ('LPX6', 'LP6A', 'LP6B', 0.8889, 1.2222), 'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162), 'O4': ('C4', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O': ('C', 'LPY1', 'LPY2', 0.82322, 1.14332), 'O7': ('C7', 'LP7A', 'LP7B', 0.8108, 1.2162), 'O8': ('C8', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O9': ('C9', 'LP9A', 'LP9B', 0.8108, 1.2162)},
'AALD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)},
'PALD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)},
'BALD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)},
'IBLD': {'O': ('C', 'LPA', 'LPB', 0.85956, 1.13122)},
'ACO': {'O1': ('C1', 'LPA', 'LPB', 0.8665, 1.07246)},
'BTON': {'O1': ('C1', 'LPA', 'LPB', 0.8665, 1.07246)},
'FORM': {'O': ('C', 'LPA', 'LPB', 0.819, 1.183), 'N': ('C', 'HC', 'HT', 0.796, 1.109)},
'ACEM': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)},
'NMA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)},
'NEA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)},
'NPA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)},
'DMA': {'O': ('C', 'LPA', 'LPB', 0.82322, 1.14332)},
'THF': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222)},
'TF2M': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222)},
'THP': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222)},
'DIOX': {'O1': ('LPX', 'LP1A', 'LP1B', 0.8889, 1.2222), 'O3': ('LPX2', 'LP2A', 'LP2B', 0.8889, 1.2222)},
'DMEE': {'O2': ('LPX', 'LP2A', 'LP2B', 0.8889, 1.2222)},
'MEET': {'O3': ('LPX', 'LP3A', 'LP3B', 0.8889, 1.2222)},
'DEET': {'O3': ('LPX', 'LP3A', 'LP3B', 0.8889, 1.2222)},
'DME': {'O2': ('LPX2', 'LP2A', 'LP2B', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'MPET': {'O2': ('LPX', 'LP2A', 'LP2B', 0.8889, 1.2222)},
'MBET': {'O2': ('LPX', 'LP2A', 'LP2B', 0.8889, 1.2222)},
'EPET': {'O3': ('LPX', 'LP3A', 'LP3B', 0.8889, 1.2222)},
'MESH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)},
'ETSH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)},
'PRSH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)},
'BUSH': {'S1': ('C1', 'LP1A', 'LP1B', 0.88, 1.32)},
'DMS': {'S1': ('C1', 'LP1A', 'LP1B', 0.7808, 1.3662)},
'EMS': {'S1': ('C1', 'LP1A', 'LP1B', 0.7808, 1.3662)},
'DMDS': {'S1': ('C1', 'LP1A', 'LP1B', 0.9208, 1.0102), 'S2': ('C2', 'LP2A', 'LP2B', 0.9208, 1.0102)},
'PHEN': {'OH': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'CRES': {'OZ': ('CZ', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'PYR': {'NZ': ('LP1', 'CE1', 'CE2', 1.1611, 0.6778)},
'PYRM': {'N1': ('LP1', 'C6', 'C2', 1.2376, 0.6648), 'N3': ('LP3', 'C4', 'C2', 1.2376, 0.6648)},
'IMID': {'NE2': ('LP1', 'CE1', 'CD2', 0.808, 1.384)},
'4MIM': {'NE2': ('LP1', 'CE1', 'CD2', 0.808, 1.384)},
'4MIE': {'ND1': ('LP1', 'CE1', 'CG', 0.808, 1.384)},
'PUR0': {'N1': ('LP1', 'C6', 'C2', 1.2376, 0.6648), 'N3': ('LP3', 'C4', 'C2', 1.2376, 0.6648), 'N7': ('LP7', 'C5', 'C8', 0.808, 1.384)},
'PUR1': {'N1': ('LP1', 'C6', 'C2', 1.2376, 0.6648), 'N3': ('LP3', 'C4', 'C2', 1.2376, 0.6648), 'N7': ('LP7', 'C4', 'C8', 0.808, 1.384)},
'MEOH': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'ETOH': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'PRO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'BUO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'PRO2': {'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)},
'BUO2': {'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)},
'PEO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'HXO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'PEO2': {'O2': ('C2', 'LP2A', 'LP2B', 0.8108, 1.2162)},
'B3MO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'CPO1': {'O1': ('C1', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'ACET': {'O1': ('C2', 'LP1A', 'LP1B', 0.7229, 1.265), 'O2': ('C2', 'LP2A', 'LP2B', 0.7229, 1.265)},
'DMP': {'O11': ('O13', 'O12', 'O14', 1.0, 0.6), 'O12': ('O14', 'O11', 'O13', 1.0, 0.6), 'O13': ('P', 'O11', 'O12', 0.6, 1.0), 'O14': ('P', 'O12', 'O11', 0.6, 1.0)},
'MP_0': {'O2': ('P1', 'LP2A', 'LP2B', 0.76473, 1.16239), 'O3': ('P1', 'LP3A', 'LP3B', 0.76473, 1.16239)},
'MP_1': {'O2': ('P1', 'LPA', 'LPB', 0.76473, 1.16239)},
'HP_1': {'O1': ('P1', 'LP1A', 'LP1B', 0.76473, 1.16239), 'O2': ('P1', 'LP2A', 'LP2B', 0.76473, 1.16239)},
'HP_2': {'O1': ('P1', 'LPA', 'LPB', 0.76473, 1.16239)},
'ETAM': {'OH1': ('C5', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'CHOL': {'OH1': ('C5', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'ACEH': {'O2': ('C2', 'LP2A', 'LP2B', 0.6968, 1.2194), 'O1': ('C2', 'LP1A', 'LP1B', 0.8108, 1.2162)},
'MAS': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)},
'EAS': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)},
'MPRO': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)},
'MBU': {'O': ('C', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OM': ('C', 'LPMA', 'LPMB', 0.8108, 1.2162)},
'FLUB': {'F6': ('C6', 'C1', 'C5', 0.75, 1.125)},
'MAM1': {'N1': ('C1', 'HN1', 'HN2', 0.85, 1.05)},
'EAM1': {'N1': ('C1', 'HN1', 'HN2', 0.85, 1.05)},
'PAM1': {'N1': ('C1', 'HN1', 'HN2', 0.85, 1.05)},
'PE': {'O1': ('O3', 'O2', 'O4', 1.0, 0.6), 'O2': ('O4', 'O1', 'O3', 1.0, 0.6), 'O3': ('P1', 'O1', 'O2', 0.6, 1.0), 'O4': ('P1', 'O2', 'O1', 0.6, 1.0)},
'PC': {'O1': ('O3', 'O2', 'O4', 1.0, 0.6), 'O2': ('O4', 'O1', 'O3', 1.0, 0.6), 'O3': ('P1', 'O1', 'O2', 0.6, 1.0), 'O4': ('P1', 'O2', 'O1', 0.6, 1.0)},
'GLYC': {'O4': ('C5', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O6': ('C5', 'LP6A', 'LP6B', 0.6968, 1.2194), 'O8': ('C9', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O10': ('C9', 'LP1A', 'LP1B', 0.6968, 1.2194)},
'GLYP': {'O4': ('C5', 'LP4A', 'LP4B', 0.8108, 1.2162), 'O6': ('C5', 'LP6A', 'LP6B', 0.6968, 1.2194), 'O8': ('C9', 'LP8A', 'LP8B', 0.8108, 1.2162), 'O10': ('C9', 'LP1A', 'LP1B', 0.6968, 1.2194), 'OP1': ('OP3', 'OP2', 'OP4', 1.0, 0.6), 'OP2': ('OP4', 'OP1', 'OP3', 1.0, 0.6), 'OP3': ('P1', 'OP1', 'OP2', 0.6, 1.0), 'OP4': ('P1', 'OP2', 'OP1', 0.6, 1.0)},
'PRPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DMPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DPPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DSPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DOPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DLPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DPPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'POPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DOPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'POPE': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
'DLPC': {'O22': ('C21', 'LP1A', 'LP1B', 0.6968, 1.2194), 'O32': ('C31', 'LP1C', 'LP1D', 0.6968, 1.2194), 'O21': ('C21', 'LPMA', 'LPMB', 0.8108, 1.2162), 'O31': ('C31', 'LPMC', 'LPMD', 0.8108, 1.2162), 'O12': ('O13', 'O11', 'O14', 1.0, 0.6), 'O11': ('O14', 'O12', 'O13', 1.0, 0.6), 'O13': ('P', 'O12', 'O11', 0.6, 1.0), 'O14': ('P', 'O11', 'O12', 0.6, 1.0)},
}
patch_anisotropies = {
'ACE': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'ACP': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'NNEU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)},
'GNNU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)},
'CTER': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)},
'CTEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)},
'CTEP': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)},
'CNEU': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'CNEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'CT1': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'CT1G': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'ASPP': {'OD1': ('CG', 'LPP1', 'LPP2', 0.6968, 1.2194), 'OD2': ('CG', 'LPP3', 'LPP4', 0.8108, 1.2162)},
'GLUP': {'OE1': ('CD', 'LPP1', 'LPP2', 0.6968, 1.2194), 'OE2': ('CD', 'LPP3', 'LPP4', 0.8108, 1.2162)},
'LSN': {'NZ': ('CE', 'HZ1', 'HZ2', 0.85, 1.05)},
'HS2': {'ND1': ('LPD1', 'CE1', 'CG', 0.808, 1.384)},
'KAC': {'OH': ('CH', 'LPA', 'LPB', 0.82322, 1.14332)},
'DACE': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'DACP': {'OY': ('CY', 'LPY1', 'LPY2', 0.82322, 1.14332)},
'DNNEU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)},
'DGNNU': {'N': ('CA', 'HT1', 'HT2', 0.85, 1.05)},
'DCTER': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)},
'DCTEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)},
'DCTEP': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)},
'DCTES': {'OT1': ('C', 'LPT1', 'LPT2', 0.7229, 1.265), 'OT2': ('C', 'LPT3', 'LPT4', 0.7229, 1.265)},
'DCNEU': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'DCNEG': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'DCNES': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'DCT1': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'DCT1G': {'OT1': ('C', 'LPT1', 'LPT2', 0.6968, 1.2194), 'OT2': ('C', 'LPT3', 'LPT4', 0.8108, 1.2162)},
'OMEA': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'OMEB': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'1AOME': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'1BOME': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O5': ('LPX5', 'LP5A', 'LP5B', 0.8889, 1.2222)},
'FOMEA': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222)},
'FOMEB': {'O1': ('LPX1', 'LPMA', 'LPMB', 0.8889, 1.2222), 'O4': ('LPX4', 'LP4A', 'LP4B', 0.8889, 1.2222)},
}
delete_anisotropies = {
'OMEA': ['O5'],
'OMEB': ['O5'],
'1AOME': ['O5'],
'1BOME': ['O5'],
'FOMEA': ['O4'],
'FOMEB': ['O4'],
}
   
residue_order = {'ALAD': 0, 'ALA': 1, 'ARG': 2, 'ASN': 3, 'ASP': 4, 'CYS': 5, 'GLN': 6, 'GLU': 7, 'GLY': 8, 'HSD': 9, 'HSE': 10, 'HSP': 11, 'ILE': 12, 'LEU': 13, 'LYS': 14, 'MET': 15, 'PHE': 16, 'PRO': 17, 'SER': 18, 'THR': 19, 'TRP': 20, 'TYR': 21, 'VAL': 22, 'ALDD': 23, 'DALA': 24, 'DARG': 25, 'DASN': 26, 'DASP': 27, 'DCYS': 28, 'DGLN': 29, 'DGLU': 30, 'DGLY': 31, 'DHSD': 32, 'DHSE': 33, 'DHSP': 34, 'DILE': 35, 'DLEU': 36, 'DLYS': 37, 'DMET': 38, 'DPHE': 39, 'DPRO': 40, 'DSER': 41, 'DTHR': 42, 'DTRP': 43, 'DTYR': 44, 'DVAL': 45, 'ALLO': 46, 'PSIC': 47, 'EGLY': 48, 'MGLYOL': 49, 'MERYOL': 50, 'DTHROL': 51, 'LTHROL': 52, 'MRIBOL': 53, 'DARAOL': 54, 'LARAOL': 55, 'MXYLOL': 56, 'MALLOL': 57, 'DALTOL': 58, 'LALTOL': 59, 'DGLUOL': 60, 'LGLUOL': 61, 'DMANOL': 62, 'LMANOL': 63, 'DGULOL': 64, 'LGULOL': 65, 'DIDIOL': 66, 'LIDIOL': 67, 'MGALOL': 68, 'AGLC': 69, 'BGLC': 70, 'AALT': 71, 'BALT': 72, 'AALL': 73, 'BALL': 74, 'AGAL': 75, 'BGAL': 76, 'AGUL': 77, 'BGUL': 78, 'AIDO': 79, 'BIDO': 80, 'AMAN': 81, 'BMAN': 82, 'ATAL': 83, 'BTAL': 84, 'ARIB': 85, 'BRIB': 86, 'AARB': 87, 'BARB': 88, 'AXYF': 89, 'BXYF': 90, 'ALYF': 91, 'BLYF': 92, 'ADEO': 93, 'BDEO': 94, 'AFRU': 95, 'BFRU': 96, 'AGALA': 97, 'BGALA': 98, 'AGLCA': 99, 'BGLCA': 100, 'AIDOA': 101, 'BIDOA': 102, 'AGLCNA': 103, 'BGLCNA': 104, 'AGALNA': 105, 'BGALNA': 106, 'AMANNA': 107, 'BMANNA': 108, 'AXYL': 109, 'BXYL': 110, 'AFUC': 111, 'BFUC': 112, 'ARHM': 113, 'BRHM': 114, 'AQUI': 115, 'BQUI': 116, 'ARHMNA': 117, 'BRHMNA': 118, 'ANE5AC': 119, 'BNE5AC': 120, 'AALD': 121, 'PALD': 122, 'BALD': 123, 'IBLD': 124, 'ACO': 125, 'BTON': 126, 'FORM': 127, 'ACEM': 128, 'NMA': 129, 'NEA': 130, 'NPA': 131, 'DMA': 132, 'THF': 133, 'TF2M': 134, 'THP': 135, 'DIOX': 136, 'DMEE': 137, 'MEET': 138, 'DEET': 139, 'DME': 140, 'MPET': 141, 'MBET': 142, 'EPET': 143, 'MESH': 144, 'ETSH': 145, 'PRSH': 146, 'BUSH': 147, 'DMS': 148, 'EMS': 149, 'DMDS': 150, 'PHEN': 151, 'CRES': 152, 'PYR': 153, 'PYRM': 154, 'IMID': 155, '4MIM': 156, '4MIE': 157, 'PUR0': 158, 'PUR1': 159, 'MEOH': 160, 'ETOH': 161, 'PRO1': 162, 'BUO1': 163, 'PRO2': 164, 'BUO2': 165, 'PEO1': 166, 'HXO1': 167, 'PEO2': 168, 'B3MO1': 169, 'CPO1': 170, 'ACET': 171, 'DMP': 172, 'MP_0': 173, 'MP_1': 174, 'HP_1': 175, 'HP_2': 176, 'ETAM': 177, 'CHOL': 178, 'ACEH': 179, 'MAS': 180, 'EAS': 181, 'MPRO': 182, 'MBU': 183, 'FLUB': 184, 'MAM1': 185, 'EAM1': 186, 'PAM1': 187, 'PE': 188, 'PC': 189, 'GLYC': 190, 'GLYP': 191, 'PRPC': 192, 'DMPC': 193, 'DPPC': 194, 'DSPC': 195, 'DOPC': 196, 'DLPE': 197, 'DPPE': 198, 'POPC': 199, 'DOPE': 200, 'POPE': 201, 'DLPC': 202} residue_order = {
patch_order = {'ACE': 0, 'ACP': 1, 'NNEU': 2, 'GNNU': 3, 'CTER': 4, 'CTEG': 5, 'CTEP': 6, 'CNEU': 7, 'CNEG': 8, 'CNES': 9, 'CT1': 10, 'CT1G': 11, 'ASPP': 12, 'GLUP': 13, 'LSN': 14, 'HS2': 15, 'KAC': 16, 'DACE': 17, 'DACP': 18, 'DNNEU': 19, 'DGNNU': 20, 'DCTER': 21, 'DCTEG': 22, 'DCTEP': 23, 'DCTES': 24, 'DCNEU': 25, 'DCNEG': 26, 'DCNES': 27, 'DCT1': 28, 'DCT1G': 29, 'OMEA': 30, 'OMEB': 31, '1AOME': 32, '1BOME': 33, 'FOMEA': 34, 'FOMEB': 35} 'ALAD': 0,
'ALA': 1,
'ARG': 2,
'ASN': 3,
'ASP': 4,
'CYS': 5,
'GLN': 6,
'GLU': 7,
'GLY': 8,
'HSD': 9,
'HSE': 10,
'HSP': 11,
'ILE': 12,
'LEU': 13,
'LYS': 14,
'MET': 15,
'PHE': 16,
'PRO': 17,
'SER': 18,
'THR': 19,
'TRP': 20,
'TYR': 21,
'VAL': 22,
'ALDD': 23,
'DALA': 24,
'DARG': 25,
'DASN': 26,
'DASP': 27,
'DCYS': 28,
'DGLN': 29,
'DGLU': 30,
'DGLY': 31,
'DHSD': 32,
'DHSE': 33,
'DHSP': 34,
'DILE': 35,
'DLEU': 36,
'DLYS': 37,
'DMET': 38,
'DPHE': 39,
'DPRO': 40,
'DSER': 41,
'DTHR': 42,
'DTRP': 43,
'DTYR': 44,
'DVAL': 45,
'ALLO': 46,
'PSIC': 47,
'EGLY': 48,
'MGLYOL': 49,
'MERYOL': 50,
'DTHROL': 51,
'LTHROL': 52,
'MRIBOL': 53,
'DARAOL': 54,
'LARAOL': 55,
'MXYLOL': 56,
'MALLOL': 57,
'DALTOL': 58,
'LALTOL': 59,
'DGLUOL': 60,
'LGLUOL': 61,
'DMANOL': 62,
'LMANOL': 63,
'DGULOL': 64,
'LGULOL': 65,
'DIDIOL': 66,
'LIDIOL': 67,
'MGALOL': 68,
'AGLC': 69,
'BGLC': 70,
'AALT': 71,
'BALT': 72,
'AALL': 73,
'BALL': 74,
'AGAL': 75,
'BGAL': 76,
'AGUL': 77,
'BGUL': 78,
'AIDO': 79,
'BIDO': 80,
'AMAN': 81,
'BMAN': 82,
'ATAL': 83,
'BTAL': 84,
'ARIB': 85,
'BRIB': 86,
'AARB': 87,
'BARB': 88,
'AXYF': 89,
'BXYF': 90,
'ALYF': 91,
'BLYF': 92,
'ADEO': 93,
'BDEO': 94,
'AFRU': 95,
'BFRU': 96,
'AGALA': 97,
'BGALA': 98,
'AGLCA': 99,
'BGLCA': 100,
'AIDOA': 101,
'BIDOA': 102,
'AGLCNA': 103,
'BGLCNA': 104,
'AGALNA': 105,
'BGALNA': 106,
'AMANNA': 107,
'BMANNA': 108,
'AXYL': 109,
'BXYL': 110,
'AFUC': 111,
'BFUC': 112,
'ARHM': 113,
'BRHM': 114,
'AQUI': 115,
'BQUI': 116,
'ARHMNA': 117,
'BRHMNA': 118,
'ANE5AC': 119,
'BNE5AC': 120,
'AALD': 121,
'PALD': 122,
'BALD': 123,
'IBLD': 124,
'ACO': 125,
'BTON': 126,
'FORM': 127,
'ACEM': 128,
'NMA': 129,
'NEA': 130,
'NPA': 131,
'DMA': 132,
'THF': 133,
'TF2M': 134,
'THP': 135,
'DIOX': 136,
'DMEE': 137,
'MEET': 138,
'DEET': 139,
'DME': 140,
'MPET': 141,
'MBET': 142,
'EPET': 143,
'MESH': 144,
'ETSH': 145,
'PRSH': 146,
'BUSH': 147,
'DMS': 148,
'EMS': 149,
'DMDS': 150,
'PHEN': 151,
'CRES': 152,
'PYR': 153,
'PYRM': 154,
'IMID': 155,
'4MIM': 156,
'4MIE': 157,
'PUR0': 158,
'PUR1': 159,
'MEOH': 160,
'ETOH': 161,
'PRO1': 162,
'BUO1': 163,
'PRO2': 164,
'BUO2': 165,
'PEO1': 166,
'HXO1': 167,
'PEO2': 168,
'B3MO1': 169,
'CPO1': 170,
'ACET': 171,
'DMP': 172,
'MP_0': 173,
'MP_1': 174,
'HP_1': 175,
'HP_2': 176,
'ETAM': 177,
'CHOL': 178,
'ACEH': 179,
'MAS': 180,
'EAS': 181,
'MPRO': 182,
'MBU': 183,
'FLUB': 184,
'MAM1': 185,
'EAM1': 186,
'PAM1': 187,
'PE': 188,
'PC': 189,
'GLYC': 190,
'GLYP': 191,
'PRPC': 192,
'DMPC': 193,
'DPPC': 194,
'DSPC': 195,
'DOPC': 196,
'DLPE': 197,
'DPPE': 198,
'POPC': 199,
'DOPE': 200,
'POPE': 201,
'DLPC': 202,
}
patch_order = {
'ACE': 0,
'ACP': 1,
'NNEU': 2,
'GNNU': 3,
'CTER': 4,
'CTEG': 5,
'CTEP': 6,
'CNEU': 7,
'CNEG': 8,
'CT1': 9,
'CT1G': 10,
'ASPP': 11,
'GLUP': 12,
'LSN': 13,
'HS2': 14,
'KAC': 15,
'DACE': 16,
'DACP': 17,
'DNNEU': 18,
'DGNNU': 19,
'DCTER': 20,
'DCTEG': 21,
'DCTEP': 22,
'DCTES': 23,
'DCNEU': 24,
'DCNEG': 25,
'DCNES': 26,
'DCT1': 27,
'DCT1G': 28,
'OMEA': 29,
'OMEB': 30,
'1AOME': 31,
'1BOME': 32,
'FOMEA': 33,
'FOMEB': 34,
}
def extract_atom_name(raw_atom_name, templates):
# Process Drude particles.
atom_name_prefix = ""
if raw_atom_name.startswith("Drude-"):
raw_atom_name = raw_atom_name[len("Drude-"):]
atom_name_prefix = "D"
# Return None to indicate an atom without template name information.
atom_name_parts = raw_atom_name.rsplit("-", maxsplit=1)
if len(atom_name_parts) &lt; 2:
return None
templates.add(atom_name_parts[0])
return f"{atom_name_prefix}{atom_name_parts[1]}"
   
residue_data = [] residue_data = []
   
for residue in topology.residues(): for residue_index, residue in enumerate(topology.residues()):
# Extract the residue or patch names and atom names from the atom type names. # Extract the residue or patch names and atom names.
templates = [] template_data = templateForResidue[residue_index]
templates = set()
if template_data is None:
# Multi-residue patch; fall back to parsing atom names because OpenMM
# leaves None in templateForResidue in this case.
atom_names = [] atom_names = []
skip_residue = False
for atom in residue.atoms(): for atom in residue.atoms():
raw_atom_name = data.atomType[atom] atom_name = extract_atom_name(data.atomType[atom], templates)
atom_is_drude = raw_atom_name.startswith("Drude-") if atom_name is None:
if atom_is_drude: # Skip residues containing atoms without template name data
atom_name_parts = raw_atom_name[len("Drude-"):].rsplit("-", maxsplit=1) # (they might be from, e.g., another solvent force field file).
atom_names.append(f"D{atom_name_parts[1]}") skip_residue = True
break
atom_names.append(atom_name)
if skip_residue:
residue_data.append(([], [], []))
continue
else: else:
atom_name_parts = raw_atom_name.rsplit("-", maxsplit=1) # Extract names from template name.
atom_names.append(atom_name_parts[1]) for template_index, template_name in enumerate(template_data.name.split("-")):
templates.append(atom_name_parts[0]) if template_index:
# Patch name.
templates.add(template_name.rsplit("_", maxsplit=1)[0])
else:
# Residue name.
templates.add(template_name)
atom_names = [template_data.atoms[data.atomTemplateIndexes[atom]].name for atom in residue.atoms()]
   
# Get all unique residue or patch names that have anisotropies. # Get all unique residue or patch names that have anisotropies.
templates = set(templates)
residue_templates = sorted( residue_templates = sorted(
(template for template in templates if template in residue_anisotropies), key=residue_order.get (template for template in templates if template in residue_anisotropies), key=residue_order.get
) )
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