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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).
.. tabularcolumns:: |l|L|
================================= ============================================
===================================== =========================================
File Parameters
================================= ============================================
===================================== =========================================
: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/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/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/tip4p2005.xml` TIP4P-2005 water model\ :cite:`Abascal2005` and ions
:file:`charmm36/tip5p.xml` TIP5P water model\ :cite:`Mahoney2000` and ions
:file:`charmm36/tip5pew.xml` TIP5P-Ew water model\ :cite:`Rick2004` and ions
================================= ============================================
:file:`charmm36_2024/water.xml` Default CHARMM water model (a modified version of TIP3P\ :cite:`Jorgensen1983`) and ions
:file:`charmm36_2024/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:file:`charmm36_2024/tip3p-pme-b.xml` TIP3P-PME-B water model\ :cite:`Price2004` and ions
:file:`charmm36_2024/tip3p-pme-f.xml` TIP3P-PME-F water model\ :cite:`Price2004` and ions
:file:`charmm36_2024/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`charmm36_2024/tip4p2005.xml` TIP4P-2005 water model\ :cite:`Abascal2005` and ions
:file:`charmm36_2024/tip5p.xml` TIP5P water model\ :cite:`Mahoney2000` 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
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:
::
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
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
missing parameters for ions in your system.
......@@ -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
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
CHARMM36, either due to a lack of support for certain CHARMM
features in `ParmEd <https://github.com/parmed/parmed>`_, or
......@@ -764,6 +771,7 @@ File Force Field
:code:`amber03.xml` Amber03\ :cite:`Duan2003`
: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` 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_2019.xml` 2019 version of the CHARMM polarizable force field\ :cite:`Lopes2013`
============================= ==================================================================================
......
wrappers/python/openmm/app/data/charmm36.xml
View file @ be646878
......@@ -103763,4 +103763,12 @@
<NBFixPair epsilon="0.8631592000000001" sigma="0.25134925534893393" type1="MG" type2="SO"/>
<NBFixPair epsilon="0.8414024" sigma="0.25219560913116723" type1="MG" type2="SS1"/>
</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>
wrappers/python/openmm/app/data/charmm36/spce.xml
View file @ be646878
......@@ -121,4 +121,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36/tip3p-pme-b.xml
View file @ be646878
......@@ -121,4 +121,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36/tip3p-pme-f.xml
View file @ be646878
......@@ -121,4 +121,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36/tip4p2005.xml
View file @ be646878
......@@ -127,4 +127,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36/tip4pew.xml
View file @ be646878
......@@ -127,4 +127,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36/tip5p.xml
View file @ be646878
......@@ -129,4 +129,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36/tip5pew.xml
View file @ be646878
......@@ -129,4 +129,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36/water.xml
View file @ be646878
......@@ -127,4 +127,12 @@
<NBFixPair epsilon="0.31388368000000005" sigma="0.2877602859593296" type1="OG2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28152399493234725" type1="OG2P1" type2="SOD"/>
</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>
wrappers/python/openmm/app/data/charmm36_2024.xml
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This source diff could not be displayed because it is too large. You can view the blob instead.
wrappers/python/openmm/app/data/charmm36_2024/spce.xml 0 → 100644
View file @ be646878
<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>
<Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str" md5hash="772b85f388766661707343bb1947dc1a" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_b.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-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>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="TP3B-OH2" />
<Type class="HT" element="H" mass="1.008" name="TP3B-H1" />
<Type class="HT" element="H" mass="1.008" name="TP3B-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="TP3B">
<Atom charge="-0.83" name="OH2" type="TP3B-OH2" />
<Atom charge="0.415" name="H1" type="TP3B-H1" />
<Atom charge="0.415" name="H2" type="TP3B-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" />
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<Atom class="OX" epsilon="0.0" sigma="1.0" />
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<Atom class="MG" epsilon="0.0" sigma="1.0" />
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<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
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<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>
<Source Source="toppar/non_charmm/toppar_water_ions_tip4p_ew.str" md5hash="50fdc364d5a9faf3dc728329548dc3ac" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_jul24.tgz">toppar/non_charmm/toppar_water_ions_tip4p_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="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>
</Info>
<AtomTypes>
<Type class="OT" element="O" mass="15.9994" name="TP4E-OH2" />
<Type class="LP" mass="0.0" name="TP4E-OM" />
<Type class="HT" element="H" mass="1.008" name="TP4E-H1" />
<Type class="HT" element="H" mass="1.008" name="TP4E-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="TP4E">
<Atom charge="0.0" name="OH2" type="TP4E-OH2" />
<Atom charge="-1.04844" name="OM" type="TP4E-OM" />
<Atom charge="0.52422" name="H1" type="TP4E-H1" />
<Atom charge="0.52422" name="H2" type="TP4E-H2" />
<Bond atomName1="OH2" atomName2="H1" />
<Bond atomName1="OH2" atomName2="H2" />
<VirtualSite atomName1="OH2" atomName2="H2" atomName3="H1" p1="0.0125" 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" />
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<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" />
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<Atom class="BI3P" epsilon="0.0" sigma="1.0" />
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<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" />
<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="0.680946" sigma="0.30965857645121914" />
<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/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>
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<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>
<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_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>
......@@ -9684,15 +9684,6 @@
<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-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="DRUD" mass="0.0" name="Drude-PROP-N" />
<Type class="HDP1B" element="H" mass="1.008" name="PROP-HT1" />
......@@ -9855,17 +9846,6 @@
<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-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="DRUD" mass="0.0" name="Drude-CT1-N" />
<Type class="HDP1A" element="H" mass="1.008" name="CT1-HN" />
......@@ -9942,16 +9922,6 @@
<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-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="DRUD" mass="0.0" name="Drude-CT3-NT" />
<Type class="HDP1A" element="H" mass="1.008" name="CT3-HNT" />
......@@ -10059,6 +10029,15 @@
<Type class="CD31DC" element="C" mass="12.011" name="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="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="DRUD" mass="0.0" name="Drude-DPROP-N" />
<Type class="HDP1B" element="H" mass="1.008" name="DPROP-HT1" />
......@@ -10169,6 +10148,17 @@
<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-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="DRUD" mass="0.0" name="Drude-DCT1-N" />
<Type class="HDP1A" element="H" mass="1.008" name="DCT1-HN" />
......@@ -10206,6 +10196,16 @@
<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-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="DRUD" mass="0.0" name="Drude-OMEA-O5" />
<Type class="CD31HA" element="C" mass="12.011" name="OMEA-C1" />
......@@ -10414,10 +10414,8 @@
<AllowPatch name="ACE_3" />
<AllowPatch name="CTER_1" />
<AllowPatch name="CNEU_1" />
<AllowPatch name="CNES_1" />
<AllowPatch name="CT1_1" />
<AllowPatch name="CT2_1" />
<AllowPatch name="CT2S_2" />
<AllowPatch name="CT3_2" />
</Residue>
<Residue name="ALA">
......@@ -10455,10 +10453,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="ARG">
......@@ -10527,14 +10523,11 @@
<ExternalBond atomName="N" />
<ExternalBond atomName="C" />
<AllowPatch name="NTER_1" />
<AllowPatch name="PROP_0" />
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="ASN">
......@@ -10587,10 +10580,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="ASP">
......@@ -10643,10 +10634,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
<AllowPatch name="ASPP_0" />
</Residue>
......@@ -10692,10 +10681,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="GLN">
......@@ -10755,10 +10742,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="GLU">
......@@ -10818,10 +10803,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
<AllowPatch name="GLUP_0" />
</Residue>
......@@ -10850,15 +10833,12 @@
<ExternalBond atomName="N" />
<ExternalBond atomName="C" />
<AllowPatch name="GNTE_0" />
<AllowPatch name="GNTS_1" />
<AllowPatch name="ACE_0" />
<AllowPatch name="GNNU_0" />
<AllowPatch name="CTEG_0" />
<AllowPatch name="CNEG_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1G_0" />
<AllowPatch name="CT2G_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="HSD">
......@@ -10920,10 +10900,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
<AllowPatch name="HS2_0" />
</Residue>
......@@ -10987,10 +10965,8 @@
<AllowPatch name="NNEU_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="HSP">
......@@ -11050,10 +11026,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="ILE">
......@@ -11112,10 +11086,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="LEU">
......@@ -11174,10 +11146,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="LYS">
......@@ -11240,14 +11210,11 @@
<ExternalBond atomName="N" />
<ExternalBond atomName="C" />
<AllowPatch name="NTER_1" />
<AllowPatch name="PROP_0" />
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
<AllowPatch name="LSN_0" />
<AllowPatch name="KAC_0" />
......@@ -11308,10 +11275,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="PHE">
......@@ -11378,10 +11343,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="PRO">
......@@ -11429,8 +11392,6 @@
<AllowPatch name="PROP_0" />
<AllowPatch name="ACE_0" />
<AllowPatch name="CTEP_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="SER">
......@@ -11475,10 +11436,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="THR">
......@@ -11530,10 +11489,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="TRP">
......@@ -11612,10 +11569,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="TYR">
......@@ -11689,10 +11644,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="VAL">
......@@ -11744,10 +11697,8 @@
<AllowPatch name="ACE_0" />
<AllowPatch name="CTER_0" />
<AllowPatch name="CNEU_0" />
<AllowPatch name="CNES_0" />
<AllowPatch name="CT1_0" />
<AllowPatch name="CT2_0" />
<AllowPatch name="CT2S_1" />
<AllowPatch name="CT3_1" />
</Residue>
<Residue name="ALLO">
......@@ -12742,7 +12693,6 @@
<VirtualSite atomName1="O" atomName2="CT" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPY1" 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="CT" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPY2" 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="ACE_2" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
<AllowPatch name="OMEA_0" />
<AllowPatch name="1AOME_0" />
......@@ -13003,7 +12953,6 @@
<VirtualSite atomName1="O" atomName2="CT" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPY1" 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="CT" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPY2" 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="ACE_2" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
<AllowPatch name="OMEA_0" />
<AllowPatch name="1AOME_0" />
......@@ -13148,7 +13097,6 @@
<VirtualSite atomName1="O9" atomName2="HO9" atomName3="C9" p1="-0.011970705016398403" p2="0.0005739964140425085" p3="0.032884232536689074" siteName="LP9A" 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="O9" atomName2="HO9" atomName3="C9" p1="-0.011970705016398403" p2="0.0005739964140425085" p3="-0.032884232536689074" siteName="LP9B" 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="ACE_2" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="ETHA">
......@@ -14583,7 +14531,6 @@
<Bond atomName1="C" atomName2="O" />
<VirtualSite atomName1="O" atomName2="HA" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="HA" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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" />
</Residue>
<Residue name="BALD">
......@@ -14621,7 +14568,6 @@
<Bond atomName1="C" atomName2="O" />
<VirtualSite atomName1="O" atomName2="HA" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="HA" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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" />
</Residue>
<Residue name="IBLD">
......@@ -14659,7 +14605,6 @@
<Bond atomName1="C" atomName2="O" />
<VirtualSite atomName1="O" atomName2="HA" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="HA" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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" />
</Residue>
<Residue name="ACO">
......@@ -14747,7 +14692,6 @@
<VirtualSite atomName1="O" atomName2="HA" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="HA" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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="ACE_1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="ACEM">
......@@ -14777,7 +14721,6 @@
<VirtualSite atomName1="O" atomName2="CL" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="CL" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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="ACE_1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="NMA">
......@@ -14814,7 +14757,6 @@
<VirtualSite atomName1="O" atomName2="CL" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="CL" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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="ACE_1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="NEA">
......@@ -14858,7 +14800,6 @@
<VirtualSite atomName1="O" atomName2="CL" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="CL" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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="ACE_1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="NPA">
......@@ -14909,7 +14850,6 @@
<VirtualSite atomName1="O" atomName2="CL" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="CL" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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="ACE_1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="DMA">
......@@ -14953,7 +14893,6 @@
<VirtualSite atomName1="O" atomName2="CL" atomName3="C" p1="-0.0005235721931185043" p2="-0.029995430854691738" p3="0" siteName="LPA" 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="CL" atomName3="C" p1="-0.0005235721931185043" p2="0.029995430854691738" p3="0" siteName="LPB" 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="ACE_1" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="THF">
......@@ -16218,7 +16157,6 @@
<Bond atomName1="CD" atomName2="HD2" />
<Bond atomName1="CD" atomName2="N" />
<Bond atomName1="N" atomName2="HN" />
<AllowPatch name="GNTS_0" />
<AllowPatch name="ACE_1" />
</Residue>
<Residue name="MEOH">
......@@ -17427,7 +17365,6 @@
<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="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" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="EAS">
......@@ -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="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" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="MPRO">
......@@ -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="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" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="MBU">
......@@ -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="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" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="FETH">
......@@ -17890,7 +17824,6 @@
<Bond atomName1="C" atomName2="H1" />
<Bond atomName1="C" atomName2="H2" />
<Bond atomName1="C" atomName2="H3" />
<AllowPatch name="CT2S_0" />
<AllowPatch name="CT3_0" />
</Residue>
<Residue name="ETO">
......@@ -21560,39 +21493,6 @@
<RemoveBond atomName1="HN" atomName2="N" />
<RemoveExternalBond atomName="N" />
</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">
<AddAtom charge="0.266" name="HT1" type="PROP-HT1" />
<AddAtom charge="0.266" name="HT2" type="PROP-HT2" />
......@@ -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="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_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">
<AddAtom charge="2.2962872001035097" name="CT" type="CT1-CT" />
<AddAtom charge="-2.3262872001035095" name="DCT" type="Drude-CT1-CT" />
......@@ -22211,51 +22060,6 @@
<ChangeAtom charge="1.6675290868987966" name="O" type="CT2G-O" />
<RemoveExternalBond atomName="C" />
</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">
<AddAtom charge="2.166666003079377" name="CAT" type="CT3-CAT" />
<AddAtom charge="-2.221666003079377" name="DCAT" type="Drude-CT3-CAT" />
......@@ -30342,8 +30146,6 @@
<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="-1.3204701080914898" 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="-2.179931223836688" 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" />
......@@ -30390,9 +30192,6 @@
<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="-1.963334406026505" 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="-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" />
......@@ -30415,9 +30214,6 @@
<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="-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="-2.221666003079377" 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" />
......@@ -30447,6 +30243,8 @@
<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="-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="-2.179931223836688" 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" />
......@@ -30479,6 +30277,9 @@
<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="-1.963334406026505" 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="-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" />
......@@ -30490,6 +30291,9 @@
<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="-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="-1.7353588402977551" 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" />
......@@ -30510,15 +30314,556 @@
import math
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, 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delete_impropers = {}
residue_impropers = {
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'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}
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}
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"
 
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),)}
# 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]}"
 
def is_valid_improper(atom_indices):
index_1, index_2, index_3, index_4 = atom_indices
......@@ -30542,23 +30887,38 @@ def find_improper(improper_types, atom_classes):
 
residue_data = []
 
for residue in topology.residues():
# Extract the residue or patch names and atom names from the atom type names.
templates = []
for residue_index, residue in enumerate(topology.residues()):
# Extract the residue or patch names and atom names.
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 = []
skip_residue = False
for atom in residue.atoms():
raw_atom_name = data.atomType[atom]
atom_is_drude = raw_atom_name.startswith("Drude-")
if atom_is_drude:
atom_name_parts = raw_atom_name[len("Drude-"):].rsplit("-", maxsplit=1)
atom_names.append(f"D{atom_name_parts[1]}")
atom_name = extract_atom_name(data.atomType[atom], templates)
if atom_name is None:
# Skip residues containing atoms without template name data
# (they might be from, e.g., another solvent force field file).
skip_residue = True
break
atom_names.append(atom_name)
if skip_residue:
residue_data.append(([], [], []))
continue
else:
atom_name_parts = raw_atom_name.rsplit("-", maxsplit=1)
atom_names.append(atom_name_parts[1])
templates.append(atom_name_parts[0])
# Extract names from template name.
for template_index, template_name in enumerate(template_data.name.split("-")):
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.
templates = set(templates)
residue_templates = sorted(
(template for template in templates if template in residue_impropers), key=residue_order.get
)
......@@ -30661,32 +31021,548 @@ if harmonic_impropers:
sys.addForce(harmonic_force)</Script>
<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)}}
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)}}
delete_anisotropies = {'OMEA': ['O5'], 'OMEB': ['O5'], '1AOME': ['O5'], '1BOME': ['O5'], 'FOMEA': ['O4'], 'FOMEB': ['O4']}
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)},
}
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}
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}
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,
}
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 = []
 
for residue in topology.residues():
# Extract the residue or patch names and atom names from the atom type names.
templates = []
for residue_index, residue in enumerate(topology.residues()):
# Extract the residue or patch names and atom names.
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 = []
skip_residue = False
for atom in residue.atoms():
raw_atom_name = data.atomType[atom]
atom_is_drude = raw_atom_name.startswith("Drude-")
if atom_is_drude:
atom_name_parts = raw_atom_name[len("Drude-"):].rsplit("-", maxsplit=1)
atom_names.append(f"D{atom_name_parts[1]}")
atom_name = extract_atom_name(data.atomType[atom], templates)
if atom_name is None:
# Skip residues containing atoms without template name data
# (they might be from, e.g., another solvent force field file).
skip_residue = True
break
atom_names.append(atom_name)
if skip_residue:
residue_data.append(([], [], []))
continue
else:
atom_name_parts = raw_atom_name.rsplit("-", maxsplit=1)
atom_names.append(atom_name_parts[1])
templates.append(atom_name_parts[0])
# Extract names from template name.
for template_index, template_name in enumerate(template_data.name.split("-")):
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.
templates = set(templates)
residue_templates = sorted(
(template for template in templates if template in residue_anisotropies), key=residue_order.get
)
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