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Commit 94e0853a authored by Evan Pretti's avatar Evan Pretti
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Copy water models from Amber14 to Amber 19 and update paths

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docs-source/usersguide/application/02_running_sims.rst
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...@@ -25,7 +25,7 @@ steps. ...@@ -25,7 +25,7 @@ steps.
from sys import stdout from sys import stdout
pdb = PDBFile('input.pdb') pdb = PDBFile('input.pdb')
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml') forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
nonbondedCutoff=1*nanometer, constraints=HBonds) nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds) integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
...@@ -87,14 +87,14 @@ Make sure you include the single quotes around the file name. OpenMM also can l ...@@ -87,14 +87,14 @@ Make sure you include the single quotes around the file name. OpenMM also can l
files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PDBxFile`. files in the newer PDBx/mmCIF format: just change :class:`PDBFile` to :class:`PDBxFile`.
:: ::
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml') forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
This line specifies the force field to use for the simulation. Force fields are This line specifies the force field to use for the simulation. Force fields are
defined by XML files. OpenMM includes XML files defining lots of standard force fields (see Section :numref:`force-fields`). defined by XML files. OpenMM includes XML files defining lots of standard force fields (see Section :numref:`force-fields`).
If you find you need to extend the repertoire of force fields available, If you find you need to extend the repertoire of force fields available,
you can find more information on how to create these XML files in Chapter :numref:`creating-force-fields`. you can find more information on how to create these XML files in Chapter :numref:`creating-force-fields`.
In this case we load two of those files: :file:`amber19-all.xml`, which contains the In this case we load two of those files: :file:`amber19-all.xml`, which contains the
Amber19 force field, and :file:`amber14/tip3pfb.xml`, which contains the TIP3P-FB water model. The Amber19 force field, and :file:`amber19/tip3pfb.xml`, which contains the TIP3P-FB water model. The
:class:`ForceField` object is assigned to a variable called :code:`forcefield`\ . :class:`ForceField` object is assigned to a variable called :code:`forcefield`\ .
:: ::
...@@ -456,7 +456,7 @@ the main force field, and possibly a second file to define the water model ...@@ -456,7 +456,7 @@ the main force field, and possibly a second file to define the water model
(either implicit or explicit). For example: (either implicit or explicit). For example:
:: ::
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml') forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
In some cases, one XML file may load several others. For example, :file:`amber19-all.xml` In some cases, one XML file may load several others. For example, :file:`amber19-all.xml`
is really just a shortcut for loading several different files that together make up is really just a shortcut for loading several different files that together make up
...@@ -488,29 +488,29 @@ File Parameters ...@@ -488,29 +488,29 @@ File Parameters
:file:`amber19/DNA.OL21.xml` DNA\ :cite:`Zgarbova2021` :file:`amber19/DNA.OL21.xml` DNA\ :cite:`Zgarbova2021`
:file:`amber14/RNA.OL3.xml` RNA :file:`amber14/RNA.OL3.xml` RNA
:file:`amber14/GLYCAM_06j-1.xml` Carbohydrates and glycosylated proteins\ :cite:`Kirschner2007` :file:`amber14/GLYCAM_06j-1.xml` Carbohydrates and glycosylated proteins\ :cite:`Kirschner2007`
:file:`amber14/tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983` and ions :file:`amber19/tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983` and ions
:file:`amber14/tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014` and ions :file:`amber19/tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions :file:`amber19/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions :file:`amber19/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions :file:`amber19/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:code:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions :file:`amber19/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:code:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions :file:`amber19/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
=================================== =========================================== =================================== ===========================================
As a convenience, the file :file:`amber19-all.xml` can be used as a shortcut to As a convenience, the file :file:`amber19-all.xml` can be used as a shortcut to
include :file:`amber19/protein.ff19SB.xml`, :file:`amber19/DNA.OL21.xml`, and include :file:`amber19/protein.ff19SB.xml`, :file:`amber19/DNA.OL21.xml`, and
:file:`amber14/RNA.OL3.xml`. In most cases, you can simply include that file, :file:`amber14/RNA.OL3.xml`. In most cases, you can simply include that file,
plus one of the water models, such as :file:`amber14/tip3pfb.xml` for the plus one of the water models, such as :file:`amber19/tip3pfb.xml` for the
TIP3P-FB water model and ions\ :cite:`Wang2014`: TIP3P-FB water model and ions\ :cite:`Wang2014`:
:: ::
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml') forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
GLYCAM is not included by default, since it is quite large. If your system contains GLYCAM is not included by default, since it is quite large. If your system contains
carbohydrates, include that file as well: carbohydrates, include that file as well:
:: ::
forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml', 'amber19/GLYCAM_06j-1.xml') forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml', 'amber14/GLYCAM_06j-1.xml')
Be aware that GLYCAM works somewhat differently from most force fields. It uses Be aware that GLYCAM works somewhat differently from most force fields. It uses
its own nonstandard `naming convention <https://glycam.org/docs/forcefield/glycam-naming-2/index.html>`_ its own nonstandard `naming convention <https://glycam.org/docs/forcefield/glycam-naming-2/index.html>`_
...@@ -524,9 +524,9 @@ to them. ...@@ -524,9 +524,9 @@ to them.
the Amber14 and Amber19 force fields and can be used with the files in the the Amber14 and Amber19 force fields and can be used with the files in the
:code:`amber19` directory. :code:`amber19` directory.
.. tip:: The solvent model XML files included under the :file:`amber14/` directory .. tip:: The solvent model XML files included under the :file:`amber19/` directory
include both water *and* ions compatible with that water model, so if you include both water *and* ions compatible with that water model, so if you
mistakenly specify :file:`tip3p.xml` instead of :file:`amber14/tip3p.xml`, mistakenly specify :file:`tip3p.xml` instead of :file:`amber19/tip3p.xml`,
you run the risk of having :class:`ForceField` throw an exception since you run the risk of having :class:`ForceField` throw an exception since
:file:`tip3p.xml` will be missing parameters for ions in your system. :file:`tip3p.xml` will be missing parameters for ions in your system.
...@@ -569,10 +569,15 @@ File Parameters ...@@ -569,10 +569,15 @@ File Parameters
:file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions :file:`amber14/tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004` and ions
:file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions :file:`amber14/tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014` and ions
:file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions :file:`amber14/spce.xml` SPC/E water model\ :cite:`Berendsen1987` and ions
:code:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions :file:`amber14/opc.xml` OPC water model\ :cite:`Izadi2014` and ions
:code:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions :file:`amber14/opc3.xml` OPC3 water model\ :cite:`Izadi2016` and ions
=================================== ============================================ =================================== ============================================
.. tip::
The XML files for water and ions provided in the :file:`amber14/` directory
are identical to those in the :file:`amber19/` directory. They are provided
in both directories for compatibility and convenience.
The converted parameter sets come from the `AmberTools 17 release <http://ambermd.org/AmberTools.php>`_ The converted parameter sets come from the `AmberTools 17 release <http://ambermd.org/AmberTools.php>`_
and were converted using the openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_. and were converted using the openmmforcefields_ package and `ParmEd <https://github.com/parmed/parmed>`_.
......
examples/simulatePdb.py
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...@@ -4,7 +4,7 @@ from openmm.unit import * ...@@ -4,7 +4,7 @@ from openmm.unit import *
from sys import stdout from sys import stdout
pdb = PDBFile('input.pdb') pdb = PDBFile('input.pdb')
forcefield = ForceField('amber19-all.xml', 'amber14/tip3pfb.xml') forcefield = ForceField('amber19-all.xml', 'amber19/tip3pfb.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds) system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds) integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
simulation = Simulation(pdb.topology, system, integrator) simulation = Simulation(pdb.topology, system, integrator)
......
wrappers/python/openmm/app/data/amber19/opc.xml 0 → 100644
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wrappers/python/openmm/app/data/amber19/opc3.xml 0 → 100644
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wrappers/python/openmm/app/data/amber19/spce.xml 0 → 100644
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<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_spce" md5hash="576c159afdaa5f4f6b05250ce4326bd3" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_spce</Source>
<Source Source="parm/frcmod.ions234lm_126_spce" md5hash="11ef85dfcf07639646dd361590b76166" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_spce</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="spce.xml" md5hash="5c815beccd16958666face51044e4a7b" sourcePackage="OpenMM" sourcePackageVersion="7.2">spce.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279-13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Berendsen, H.J.C., Grigera, J.R., and Straatsma, T.P. (1987). The missing term in effective pair potentials. J. Phys. Chem. 91, 6269-6271.</Reference>
</Info>
<AtomTypes>
<Type class="spce_standard-Li+" element="Li" mass="6.94" name="spce_standard-Li+"/>
<Type class="spce_standard-Na+" element="Na" mass="22.99" name="spce_standard-Na+"/>
<Type class="spce_standard-K+" element="K" mass="39.1" name="spce_standard-K+"/>
<Type class="spce_standard-Rb+" element="Rb" mass="85.47" name="spce_standard-Rb+"/>
<Type class="spce_standard-Cs+" element="Cs" mass="132.91" name="spce_standard-Cs+"/>
<Type class="spce_standard-F-" element="F" mass="19.0" name="spce_standard-F-"/>
<Type class="spce_standard-Cl-" element="Cl" mass="35.45" name="spce_standard-Cl-"/>
<Type class="spce_standard-Br-" element="Br" mass="79.9" name="spce_standard-Br-"/>
<Type class="spce_standard-I-" element="I" mass="126.9" name="spce_standard-I-"/>
<Type class="spce_standard-Be2+" element="Be" mass="9.01" name="spce_standard-Be2+"/>
<Type class="spce_standard-Cu2+" element="Cu" mass="63.55" name="spce_standard-Cu2+"/>
<Type class="spce_standard-Ni2+" element="Ni" mass="58.69" name="spce_standard-Ni2+"/>
<Type class="spce_standard-Pt2+" element="Pt" mass="195.08" name="spce_standard-Pt2+"/>
<Type class="spce_standard-Zn2+" element="Zn" mass="65.4" name="spce_standard-Zn2+"/>
<Type class="spce_standard-Co2+" element="Co" mass="58.93" name="spce_standard-Co2+"/>
<Type class="spce_standard-Pd2+" element="Pd" mass="106.42" name="spce_standard-Pd2+"/>
<Type class="spce_standard-Ag2+" element="Ag" mass="107.87" name="spce_standard-Ag2+"/>
<Type class="spce_standard-Cr2+" element="Cr" mass="52.0" name="spce_standard-Cr2+"/>
<Type class="spce_standard-Fe2+" element="Fe" mass="55.85" name="spce_standard-Fe2+"/>
<Type class="spce_standard-Mg2+" element="Mg" mass="24.305" name="spce_standard-Mg2+"/>
<Type class="spce_standard-V2+" element="V" mass="50.94" name="spce_standard-V2+"/>
<Type class="spce_standard-Mn2+" element="Mn" mass="54.94" name="spce_standard-Mn2+"/>
<Type class="spce_standard-Hg2+" element="Hg" mass="200.59" name="spce_standard-Hg2+"/>
<Type class="spce_standard-Cd2+" element="Cd" mass="112.41" name="spce_standard-Cd2+"/>
<Type class="spce_standard-Yb2+" element="Yb" mass="173.05" name="spce_standard-Yb2+"/>
<Type class="spce_standard-Ca2+" element="Ca" mass="40.08" name="spce_standard-Ca2+"/>
<Type class="spce_standard-Sn2+" element="Sn" mass="118.71" name="spce_standard-Sn2+"/>
<Type class="spce_standard-Pb2+" element="Pb" mass="207.2" name="spce_standard-Pb2+"/>
<Type class="spce_standard-Eu2+" element="Eu" mass="151.96" name="spce_standard-Eu2+"/>
<Type class="spce_standard-Sr2+" element="Sr" mass="87.62" name="spce_standard-Sr2+"/>
<Type class="spce_standard-Sm2+" element="Sm" mass="150.36" name="spce_standard-Sm2+"/>
<Type class="spce_standard-Ba2+" element="Ba" mass="137.33" name="spce_standard-Ba2+"/>
<Type class="spce_standard-Ra2+" element="Ra" mass="226.03" name="spce_standard-Ra2+"/>
<Type class="spce_standard-Al3+" element="Al" mass="26.98" name="spce_standard-Al3+"/>
<Type class="spce_standard-Fe3+" element="Fe" mass="55.85" name="spce_standard-Fe3+"/>
<Type class="spce_standard-Cr3+" element="Cr" mass="52.0" name="spce_standard-Cr3+"/>
<Type class="spce_standard-In3+" element="In" mass="114.82" name="spce_standard-In3+"/>
<Type class="spce_standard-Tl3+" element="Tl" mass="204.38" name="spce_standard-Tl3+"/>
<Type class="spce_standard-Y3+" element="Y" mass="88.91" name="spce_standard-Y3+"/>
<Type class="spce_standard-La3+" element="La" mass="138.91" name="spce_standard-La3+"/>
<Type class="spce_standard-Ce3+" element="Ce" mass="140.12" name="spce_standard-Ce3+"/>
<Type class="spce_standard-Pr3+" element="Pr" mass="140.91" name="spce_standard-Pr3+"/>
<Type class="spce_standard-Nd3+" element="Nd" mass="144.24" name="spce_standard-Nd3+"/>
<Type class="spce_standard-Sm3+" element="Sm" mass="150.36" name="spce_standard-Sm3+"/>
<Type class="spce_standard-Eu3+" element="Eu" mass="151.96" name="spce_standard-Eu3+"/>
<Type class="spce_standard-Gd3+" element="Gd" mass="157.25" name="spce_standard-Gd3+"/>
<Type class="spce_standard-Tb3+" element="Tb" mass="158.93" name="spce_standard-Tb3+"/>
<Type class="spce_standard-Dy3+" element="Dy" mass="162.5" name="spce_standard-Dy3+"/>
<Type class="spce_standard-Er3+" element="Er" mass="167.26" name="spce_standard-Er3+"/>
<Type class="spce_standard-Tm3+" element="Tm" mass="168.93" name="spce_standard-Tm3+"/>
<Type class="spce_standard-Lu3+" element="Lu" mass="174.97" name="spce_standard-Lu3+"/>
<Type class="spce_standard-Hf4+" element="Hf" mass="178.49" name="spce_standard-Hf4+"/>
<Type class="spce_standard-Zr4+" element="Zr" mass="91.22" name="spce_standard-Zr4+"/>
<Type class="spce_standard-Ce4+" element="Ce" mass="140.12" name="spce_standard-Ce4+"/>
<Type class="spce_standard-U4+" element="U" mass="238.03" name="spce_standard-U4+"/>
<Type class="spce_standard-Pu4+" element="Pu" mass="244.06" name="spce_standard-Pu4+"/>
<Type class="spce_standard-Th4+" element="Th" mass="232.04" name="spce_standard-Th4+"/>
<Type name="spce-O" class="spce-O" element="O" mass="15.99943"/>
<Type name="spce-H" class="spce-H" element="H" mass="1.007947"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="spce_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="spce_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="spce_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="spce_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="spce_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="spce_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="spce_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="spce_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="spce_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="spce_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="spce_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="spce_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="spce_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="spce_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="spce_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="spce_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="spce_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="spce_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="spce_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="spce_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="spce_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="spce_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="spce_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="spce_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="spce_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="spce_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="spce_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="spce_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="spce_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="spce_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="spce_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="spce_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="spce_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="spce_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="spce_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="spce_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="spce_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="spce_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="spce_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="spce_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="spce_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="spce_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="spce_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="spce_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="spce_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="spce_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="spce_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="spce_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="spce_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="spce_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="spce_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="spce_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="spce_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="spce_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="spce_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="spce_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="spce_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="spce-O" charge="-0.8476"/>
<Atom name="H1" type="spce-H" charge="0.4238"/>
<Atom name="H2" type="spce-H" charge="0.4238"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="spce-O" type2="spce-H" length="0.1" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="spce-H" type2="spce-O" type3="spce-H" angle="1.91061193216" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="1.4088967296000001" sigma="0.14094017720980168" type="spce_standard-Li+"/>
<Atom epsilon="1.4754532912" sigma="0.21595384927721822" type="spce_standard-Na+"/>
<Atom epsilon="1.7978873936000002" sigma="0.2838403315995121" type="spce_standard-K+"/>
<Atom epsilon="1.8623134624" sigma="0.3094982146819539" type="spce_standard-Rb+"/>
<Atom epsilon="0.37595959600000006" sigma="0.36010126187232516" type="spce_standard-Cs+"/>
<Atom epsilon="0.030963692" sigma="0.4021516813685492" type="spce_standard-F-"/>
<Atom epsilon="0.05349244" sigma="0.48304528497569194" type="spce_standard-Cl-"/>
<Atom epsilon="0.1127947824" sigma="0.4901724747208147" type="spce_standard-Br-"/>
<Atom epsilon="0.179010348" sigma="0.5201066716503301" type="spce_standard-I-"/>
<Atom epsilon="1.92464e-05" sigma="0.1712307336265732" type="spce_standard-Be2+"/>
<Atom epsilon="0.0067303824" sigma="0.21791382645712698" type="spce_standard-Cu2+"/>
<Atom epsilon="0.01065702456" sigma="0.223259218765969" type="spce_standard-Ni2+"/>
<Atom epsilon="0.014015354" sigma="0.22664463389490233" type="spce_standard-Pt2+"/>
<Atom epsilon="0.014823368080000001" sigma="0.2273573528694146" type="spce_standard-Zn2+"/>
<Atom epsilon="0.0218984284" sigma="0.23252456543462854" type="spce_standard-Co2+"/>
<Atom epsilon="0.0218984284" sigma="0.23252456543462854" type="spce_standard-Pd2+"/>
<Atom epsilon="0.03264699888" sigma="0.23822631723072674" type="spce_standard-Ag2+"/>
<Atom epsilon="0.03718454688" sigma="0.2401862944106355" type="spce_standard-Cr2+"/>
<Atom epsilon="0.03986113536" sigma="0.2412553728724039" type="spce_standard-Fe2+"/>
<Atom epsilon="0.042686716080000006" sigma="0.2423244513341723" type="spce_standard-Mg2+"/>
<Atom epsilon="0.045158958000000006" sigma="0.24321535005231262" type="spce_standard-V2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="spce_standard-Mn2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="spce_standard-Hg2+"/>
<Atom epsilon="0.07419972544" sigma="0.2515897980028318" type="spce_standard-Cd2+"/>
<Atom epsilon="0.40718273784000003" sigma="0.2911457010882629" type="spce_standard-Yb2+"/>
<Atom epsilon="0.40953067312" sigma="0.2913238808318909" type="spce_standard-Ca2+"/>
<Atom epsilon="0.44813803104000005" sigma="0.29417475672994003" type="spce_standard-Sn2+"/>
<Atom epsilon="0.669006956" sigma="0.3084291362201855" type="spce_standard-Pb2+"/>
<Atom epsilon="0.8445052544000001" sigma="0.31822902211972925" type="spce_standard-Eu2+"/>
<Atom epsilon="0.8713768270400001" sigma="0.31965446006875375" type="spce_standard-Sr2+"/>
<Atom epsilon="0.89173069" sigma="0.32072353853052216" type="spce_standard-Sm2+"/>
<Atom epsilon="1.55336865968" sigma="0.35279589238357434" type="spce_standard-Ba2+"/>
<Atom epsilon="1.55336865968" sigma="0.35279589238357434" type="spce_standard-Ra2+"/>
<Atom epsilon="0.019458696160000004" sigma="0.23092094774197594" type="spce_standard-Al3+"/>
<Atom epsilon="0.05678093848" sigma="0.24695712466850203" type="spce_standard-Fe3+"/>
<Atom epsilon="0.035064095680000004" sigma="0.23929539569249514" type="spce_standard-Cr3+"/>
<Atom epsilon="0.11751709584" sigma="0.26032060544060714" type="spce_standard-In3+"/>
<Atom epsilon="0.18079185336" sigma="0.26958595210926667" type="spce_standard-Tl3+"/>
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="spce_standard-Y3+"/>
<Atom epsilon="0.63014479248" sigma="0.3061127995530206" type="spce_standard-La3+"/>
<Atom epsilon="0.69962078192" sigma="0.3102109336564662" type="spce_standard-Ce3+"/>
<Atom epsilon="0.6781265697600001" sigma="0.3089636754510697" type="spce_standard-Pr3+"/>
<Atom epsilon="0.52569060488" sigma="0.2995201490387821" type="spce_standard-Nd3+"/>
<Atom epsilon="0.46816830344000004" sigma="0.2956001946789646" type="spce_standard-Sm3+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="spce_standard-Eu3+"/>
<Atom epsilon="0.38186547936" sigma="0.2891857239083541" type="spce_standard-Gd3+"/>
<Atom epsilon="0.39786810784" sigma="0.29043298211375057" type="spce_standard-Tb3+"/>
<Atom epsilon="0.35100580160000006" sigma="0.28669120749756116" type="spce_standard-Dy3+"/>
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="spce_standard-Er3+"/>
<Atom epsilon="0.33615222504000003" sigma="0.2854439492921647" type="spce_standard-Tm3+"/>
<Atom epsilon="0.30760316128000004" sigma="0.28294943288137175" type="spce_standard-Lu3+"/>
<Atom epsilon="0.16448090592" sigma="0.26744779518572986" type="spce_standard-Hf4+"/>
<Atom epsilon="0.19225856560000001" sigma="0.2710113900582912" type="spce_standard-Zr4+"/>
<Atom epsilon="0.5474740988000001" sigma="0.3009455869878066" type="spce_standard-Ce4+"/>
<Atom epsilon="0.5474740988000001" sigma="0.3009455869878066" type="spce_standard-U4+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="spce_standard-Pu4+"/>
<Atom epsilon="0.61548811496" sigma="0.30522190083488027" type="spce_standard-Th4+"/>
<Atom type="spce-O" sigma="0.31657195050398818" epsilon="0.6497752"/>
<Atom type="spce-H" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/amber19/tip3p.xml 0 → 100644
View file @ 94e0853a
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip3p" md5hash="0e5e74a17e42382511afd4116f70ff16" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip3p</Source>
<Source Source="parm/frcmod.ions234lm_126_tip3p" md5hash="69bb41a7702e76fb9f5ef041d063dfae" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip3p</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip3p.xml" md5hash="dde8c717e8d77c7511b575779ac9f968" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip3p.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279-13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., and Klein, M.L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics 79, 926-935.</Reference>
</Info>
<AtomTypes>
<Type class="tip3p_standard-Li+" element="Li" mass="6.94" name="tip3p_standard-Li+"/>
<Type class="tip3p_standard-Na+" element="Na" mass="22.99" name="tip3p_standard-Na+"/>
<Type class="tip3p_standard-K+" element="K" mass="39.1" name="tip3p_standard-K+"/>
<Type class="tip3p_standard-Rb+" element="Rb" mass="85.47" name="tip3p_standard-Rb+"/>
<Type class="tip3p_standard-Cs+" element="Cs" mass="132.91" name="tip3p_standard-Cs+"/>
<Type class="tip3p_standard-F-" element="F" mass="19.0" name="tip3p_standard-F-"/>
<Type class="tip3p_standard-Cl-" element="Cl" mass="35.45" name="tip3p_standard-Cl-"/>
<Type class="tip3p_standard-Br-" element="Br" mass="79.9" name="tip3p_standard-Br-"/>
<Type class="tip3p_standard-I-" element="I" mass="126.9" name="tip3p_standard-I-"/>
<Type class="tip3p_standard-Be2+" element="Be" mass="9.01" name="tip3p_standard-Be2+"/>
<Type class="tip3p_standard-Cu2+" element="Cu" mass="63.55" name="tip3p_standard-Cu2+"/>
<Type class="tip3p_standard-Ni2+" element="Ni" mass="58.69" name="tip3p_standard-Ni2+"/>
<Type class="tip3p_standard-Pt2+" element="Pt" mass="195.08" name="tip3p_standard-Pt2+"/>
<Type class="tip3p_standard-Zn2+" element="Zn" mass="65.4" name="tip3p_standard-Zn2+"/>
<Type class="tip3p_standard-Co2+" element="Co" mass="58.93" name="tip3p_standard-Co2+"/>
<Type class="tip3p_standard-Pd2+" element="Pd" mass="106.42" name="tip3p_standard-Pd2+"/>
<Type class="tip3p_standard-Ag2+" element="Ag" mass="107.87" name="tip3p_standard-Ag2+"/>
<Type class="tip3p_standard-Cr2+" element="Cr" mass="52.0" name="tip3p_standard-Cr2+"/>
<Type class="tip3p_standard-Fe2+" element="Fe" mass="55.85" name="tip3p_standard-Fe2+"/>
<Type class="tip3p_standard-Mg2+" element="Mg" mass="24.305" name="tip3p_standard-Mg2+"/>
<Type class="tip3p_standard-V2+" element="V" mass="50.94" name="tip3p_standard-V2+"/>
<Type class="tip3p_standard-Mn2+" element="Mn" mass="54.94" name="tip3p_standard-Mn2+"/>
<Type class="tip3p_standard-Hg2+" element="Hg" mass="200.59" name="tip3p_standard-Hg2+"/>
<Type class="tip3p_standard-Cd2+" element="Cd" mass="112.41" name="tip3p_standard-Cd2+"/>
<Type class="tip3p_standard-Yb2+" element="Yb" mass="173.05" name="tip3p_standard-Yb2+"/>
<Type class="tip3p_standard-Ca2+" element="Ca" mass="40.08" name="tip3p_standard-Ca2+"/>
<Type class="tip3p_standard-Sn2+" element="Sn" mass="118.71" name="tip3p_standard-Sn2+"/>
<Type class="tip3p_standard-Pb2+" element="Pb" mass="207.2" name="tip3p_standard-Pb2+"/>
<Type class="tip3p_standard-Eu2+" element="Eu" mass="151.96" name="tip3p_standard-Eu2+"/>
<Type class="tip3p_standard-Sr2+" element="Sr" mass="87.62" name="tip3p_standard-Sr2+"/>
<Type class="tip3p_standard-Sm2+" element="Sm" mass="150.36" name="tip3p_standard-Sm2+"/>
<Type class="tip3p_standard-Ba2+" element="Ba" mass="137.33" name="tip3p_standard-Ba2+"/>
<Type class="tip3p_standard-Ra2+" element="Ra" mass="226.03" name="tip3p_standard-Ra2+"/>
<Type class="tip3p_standard-Al3+" element="Al" mass="26.98" name="tip3p_standard-Al3+"/>
<Type class="tip3p_standard-Fe3+" element="Fe" mass="55.85" name="tip3p_standard-Fe3+"/>
<Type class="tip3p_standard-Cr3+" element="Cr" mass="52.0" name="tip3p_standard-Cr3+"/>
<Type class="tip3p_standard-In3+" element="In" mass="114.82" name="tip3p_standard-In3+"/>
<Type class="tip3p_standard-Tl3+" element="Tl" mass="204.38" name="tip3p_standard-Tl3+"/>
<Type class="tip3p_standard-Y3+" element="Y" mass="88.91" name="tip3p_standard-Y3+"/>
<Type class="tip3p_standard-La3+" element="La" mass="138.91" name="tip3p_standard-La3+"/>
<Type class="tip3p_standard-Ce3+" element="Ce" mass="140.12" name="tip3p_standard-Ce3+"/>
<Type class="tip3p_standard-Pr3+" element="Pr" mass="140.91" name="tip3p_standard-Pr3+"/>
<Type class="tip3p_standard-Nd3+" element="Nd" mass="144.24" name="tip3p_standard-Nd3+"/>
<Type class="tip3p_standard-Sm3+" element="Sm" mass="150.36" name="tip3p_standard-Sm3+"/>
<Type class="tip3p_standard-Eu3+" element="Eu" mass="151.96" name="tip3p_standard-Eu3+"/>
<Type class="tip3p_standard-Gd3+" element="Gd" mass="157.25" name="tip3p_standard-Gd3+"/>
<Type class="tip3p_standard-Tb3+" element="Tb" mass="158.93" name="tip3p_standard-Tb3+"/>
<Type class="tip3p_standard-Dy3+" element="Dy" mass="162.5" name="tip3p_standard-Dy3+"/>
<Type class="tip3p_standard-Er3+" element="Er" mass="167.26" name="tip3p_standard-Er3+"/>
<Type class="tip3p_standard-Tm3+" element="Tm" mass="168.93" name="tip3p_standard-Tm3+"/>
<Type class="tip3p_standard-Lu3+" element="Lu" mass="174.97" name="tip3p_standard-Lu3+"/>
<Type class="tip3p_standard-Hf4+" element="Hf" mass="178.49" name="tip3p_standard-Hf4+"/>
<Type class="tip3p_standard-Zr4+" element="Zr" mass="91.22" name="tip3p_standard-Zr4+"/>
<Type class="tip3p_standard-Ce4+" element="Ce" mass="140.12" name="tip3p_standard-Ce4+"/>
<Type class="tip3p_standard-U4+" element="U" mass="238.03" name="tip3p_standard-U4+"/>
<Type class="tip3p_standard-Pu4+" element="Pu" mass="244.06" name="tip3p_standard-Pu4+"/>
<Type class="tip3p_standard-Th4+" element="Th" mass="232.04" name="tip3p_standard-Th4+"/>
<Type name="tip3p-O" class="tip3p-O" element="O" mass="15.99943"/>
<Type name="tip3p-H" class="tip3p-H" element="H" mass="1.007947"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip3p_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip3p_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip3p_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip3p_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip3p_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip3p_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip3p_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip3p_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip3p_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip3p_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip3p_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip3p_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip3p_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip3p_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip3p_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip3p_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip3p_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip3p_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip3p_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip3p_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip3p_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip3p_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip3p_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip3p_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip3p_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip3p_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip3p_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip3p_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip3p_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip3p_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip3p_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip3p_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip3p_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip3p_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip3p_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip3p_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip3p_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip3p_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip3p_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip3p_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip3p_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip3p_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip3p_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip3p_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip3p_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip3p_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip3p_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip3p_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip3p_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip3p_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip3p_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip3p_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip3p_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip3p_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip3p_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip3p_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip3p_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip3p-O" charge="-0.834"/>
<Atom name="H1" type="tip3p-H" charge="0.417"/>
<Atom name="H2" type="tip3p-H" charge="0.417"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip3p-O" type2="tip3p-H" length="0.09572" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip3p-H" type2="tip3p-O" type3="tip3p-H" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.1171084864" sigma="0.18263423721876956" type="tip3p_standard-Li+"/>
<Atom epsilon="0.3658460312" sigma="0.2439280690268249" type="tip3p_standard-Na+"/>
<Atom epsilon="0.8103692536" sigma="0.3037964628858557" type="tip3p_standard-K+"/>
<Atom epsilon="1.3716068296000001" sigma="0.32303987519768707" type="tip3p_standard-Rb+"/>
<Atom epsilon="1.7009608496" sigma="0.3520831734090621" type="tip3p_standard-Cs+"/>
<Atom epsilon="0.014074976" sigma="0.4103479495754403" type="tip3p_standard-F-"/>
<Atom epsilon="0.14891274399999999" sigma="0.4477656957373345" type="tip3p_standard-Cl-"/>
<Atom epsilon="0.24541419360000002" sigma="0.46469277138200105" type="tip3p_standard-Br-"/>
<Atom epsilon="0.22460381440000002" sigma="0.5095940667762741" type="tip3p_standard-I-"/>
<Atom epsilon="1.6526800000000002e-05" sigma="0.17033983490843285" type="tip3p_standard-Be2+"/>
<Atom epsilon="0.00621311448" sigma="0.21702292773898668" type="tip3p_standard-Cu2+"/>
<Atom epsilon="0.0109754688" sigma="0.22361557825322517" type="tip3p_standard-Ni2+"/>
<Atom epsilon="0.01287174128" sigma="0.22557555543313393" type="tip3p_standard-Pt2+"/>
<Atom epsilon="0.01381916624" sigma="0.22646645415127425" type="tip3p_standard-Zn2+"/>
<Atom epsilon="0.02024604128" sigma="0.23145548697286014" type="tip3p_standard-Co2+"/>
<Atom epsilon="0.021335931440000004" sigma="0.23216820594737242" type="tip3p_standard-Pd2+"/>
<Atom epsilon="0.032257342960000004" sigma="0.2380481374870987" type="tip3p_standard-Ag2+"/>
<Atom epsilon="0.03632456752" sigma="0.23982993492337937" type="tip3p_standard-Cr2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip3p_standard-Fe2+"/>
<Atom epsilon="0.042686716080000006" sigma="0.2423244513341723" type="tip3p_standard-Mg2+"/>
<Atom epsilon="0.04465579016" sigma="0.24303717030868457" type="tip3p_standard-V2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3p_standard-Mn2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3p_standard-Hg2+"/>
<Atom epsilon="0.07419972544" sigma="0.2515897980028318" type="tip3p_standard-Cd2+"/>
<Atom epsilon="0.426181194" sigma="0.29257113903728743" type="tip3p_standard-Yb2+"/>
<Atom epsilon="0.4432056808" sigma="0.29381839724268394" type="tip3p_standard-Ca2+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="tip3p_standard-Sn2+"/>
<Atom epsilon="0.71203621616" sigma="0.31092365263097843" type="tip3p_standard-Pb2+"/>
<Atom epsilon="0.8985523254400001" sigma="0.3210798980177783" type="tip3p_standard-Eu2+"/>
<Atom epsilon="0.92601852816" sigma="0.32250533596680286" type="tip3p_standard-Sr2+"/>
<Atom epsilon="0.95724882464" sigma="0.32410895365945547" type="tip3p_standard-Sm2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3p_standard-Ba2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3p_standard-Ra2+"/>
<Atom epsilon="0.04721589608000001" sigma="0.2439280690268249" type="tip3p_standard-Al3+"/>
<Atom epsilon="0.09989325104" sigma="0.25711337005530194" type="tip3p_standard-Fe3+"/>
<Atom epsilon="0.07644268416000001" sigma="0.252124337233716" type="tip3p_standard-Cr3+"/>
<Atom epsilon="0.15168878616" sigma="0.2656659977494492" type="tip3p_standard-In3+"/>
<Atom epsilon="0.27501557520000003" sigma="0.2799203772396946" type="tip3p_standard-Tl3+"/>
<Atom epsilon="0.39786810784" sigma="0.29043298211375057" type="tip3p_standard-Y3+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip3p_standard-La3+"/>
<Atom epsilon="0.83118754056" sigma="0.31751630314521695" type="tip3p_standard-Ce3+"/>
<Atom epsilon="0.8245589130400001" sigma="0.31715994365796085" type="tip3p_standard-Pr3+"/>
<Atom epsilon="0.64794725224" sigma="0.307181878014789" type="tip3p_standard-Nd3+"/>
<Atom epsilon="0.60967151816" sigma="0.3048655413476241" type="tip3p_standard-Sm3+"/>
<Atom epsilon="0.62426246504" sigma="0.3057564400657644" type="tip3p_standard-Eu3+"/>
<Atom epsilon="0.46563832232" sigma="0.29542201493533654" type="tip3p_standard-Gd3+"/>
<Atom epsilon="0.4991058036" sigma="0.2977383516025014" type="tip3p_standard-Tb3+"/>
<Atom epsilon="0.41424963936000003" sigma="0.29168024031914713" type="tip3p_standard-Dy3+"/>
<Atom epsilon="0.40953067312" sigma="0.2913238808318909" type="tip3p_standard-Er3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip3p_standard-Tm3+"/>
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="tip3p_standard-Lu3+"/>
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="tip3p_standard-Hf4+"/>
<Atom epsilon="0.35100580160000006" sigma="0.28669120749756116" type="tip3p_standard-Zr4+"/>
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="tip3p_standard-Ce4+"/>
<Atom epsilon="0.8646299178400001" sigma="0.31929810058149766" type="tip3p_standard-U4+"/>
<Atom epsilon="0.73399083568" sigma="0.3121709108363749" type="tip3p_standard-Pu4+"/>
<Atom epsilon="0.7917259353600001" sigma="0.31537814622168014" type="tip3p_standard-Th4+"/>
<Atom type="tip3p-O" sigma="0.31507524065751241" epsilon="0.635968"/>
<Atom type="tip3p-H" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/amber19/tip3pfb.xml 0 → 100644
View file @ 94e0853a
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip3p" md5hash="0e5e74a17e42382511afd4116f70ff16" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip3p</Source>
<Source Source="parm/frcmod.ions234lm_126_tip3p" md5hash="69bb41a7702e76fb9f5ef041d063dfae" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip3p</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip3pfb.xml" md5hash="a7d1cb77f6a2d5ae69d7cd2b29bdfbf7" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip3pfb.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279-13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. (2014). Building force fields - an automatic, systematic and reproducible approach. Journal of Physical Chemistry Letters, 5, 1885-1891.</Reference>
</Info>
<AtomTypes>
<Type class="tip3pfb_standard-Li+" element="Li" mass="6.94" name="tip3pfb_standard-Li+"/>
<Type class="tip3pfb_standard-Na+" element="Na" mass="22.99" name="tip3pfb_standard-Na+"/>
<Type class="tip3pfb_standard-K+" element="K" mass="39.1" name="tip3pfb_standard-K+"/>
<Type class="tip3pfb_standard-Rb+" element="Rb" mass="85.47" name="tip3pfb_standard-Rb+"/>
<Type class="tip3pfb_standard-Cs+" element="Cs" mass="132.91" name="tip3pfb_standard-Cs+"/>
<Type class="tip3pfb_standard-F-" element="F" mass="19.0" name="tip3pfb_standard-F-"/>
<Type class="tip3pfb_standard-Cl-" element="Cl" mass="35.45" name="tip3pfb_standard-Cl-"/>
<Type class="tip3pfb_standard-Br-" element="Br" mass="79.9" name="tip3pfb_standard-Br-"/>
<Type class="tip3pfb_standard-I-" element="I" mass="126.9" name="tip3pfb_standard-I-"/>
<Type class="tip3pfb_standard-Be2+" element="Be" mass="9.01" name="tip3pfb_standard-Be2+"/>
<Type class="tip3pfb_standard-Cu2+" element="Cu" mass="63.55" name="tip3pfb_standard-Cu2+"/>
<Type class="tip3pfb_standard-Ni2+" element="Ni" mass="58.69" name="tip3pfb_standard-Ni2+"/>
<Type class="tip3pfb_standard-Pt2+" element="Pt" mass="195.08" name="tip3pfb_standard-Pt2+"/>
<Type class="tip3pfb_standard-Zn2+" element="Zn" mass="65.4" name="tip3pfb_standard-Zn2+"/>
<Type class="tip3pfb_standard-Co2+" element="Co" mass="58.93" name="tip3pfb_standard-Co2+"/>
<Type class="tip3pfb_standard-Pd2+" element="Pd" mass="106.42" name="tip3pfb_standard-Pd2+"/>
<Type class="tip3pfb_standard-Ag2+" element="Ag" mass="107.87" name="tip3pfb_standard-Ag2+"/>
<Type class="tip3pfb_standard-Cr2+" element="Cr" mass="52.0" name="tip3pfb_standard-Cr2+"/>
<Type class="tip3pfb_standard-Fe2+" element="Fe" mass="55.85" name="tip3pfb_standard-Fe2+"/>
<Type class="tip3pfb_standard-Mg2+" element="Mg" mass="24.305" name="tip3pfb_standard-Mg2+"/>
<Type class="tip3pfb_standard-V2+" element="V" mass="50.94" name="tip3pfb_standard-V2+"/>
<Type class="tip3pfb_standard-Mn2+" element="Mn" mass="54.94" name="tip3pfb_standard-Mn2+"/>
<Type class="tip3pfb_standard-Hg2+" element="Hg" mass="200.59" name="tip3pfb_standard-Hg2+"/>
<Type class="tip3pfb_standard-Cd2+" element="Cd" mass="112.41" name="tip3pfb_standard-Cd2+"/>
<Type class="tip3pfb_standard-Yb2+" element="Yb" mass="173.05" name="tip3pfb_standard-Yb2+"/>
<Type class="tip3pfb_standard-Ca2+" element="Ca" mass="40.08" name="tip3pfb_standard-Ca2+"/>
<Type class="tip3pfb_standard-Sn2+" element="Sn" mass="118.71" name="tip3pfb_standard-Sn2+"/>
<Type class="tip3pfb_standard-Pb2+" element="Pb" mass="207.2" name="tip3pfb_standard-Pb2+"/>
<Type class="tip3pfb_standard-Eu2+" element="Eu" mass="151.96" name="tip3pfb_standard-Eu2+"/>
<Type class="tip3pfb_standard-Sr2+" element="Sr" mass="87.62" name="tip3pfb_standard-Sr2+"/>
<Type class="tip3pfb_standard-Sm2+" element="Sm" mass="150.36" name="tip3pfb_standard-Sm2+"/>
<Type class="tip3pfb_standard-Ba2+" element="Ba" mass="137.33" name="tip3pfb_standard-Ba2+"/>
<Type class="tip3pfb_standard-Ra2+" element="Ra" mass="226.03" name="tip3pfb_standard-Ra2+"/>
<Type class="tip3pfb_standard-Al3+" element="Al" mass="26.98" name="tip3pfb_standard-Al3+"/>
<Type class="tip3pfb_standard-Fe3+" element="Fe" mass="55.85" name="tip3pfb_standard-Fe3+"/>
<Type class="tip3pfb_standard-Cr3+" element="Cr" mass="52.0" name="tip3pfb_standard-Cr3+"/>
<Type class="tip3pfb_standard-In3+" element="In" mass="114.82" name="tip3pfb_standard-In3+"/>
<Type class="tip3pfb_standard-Tl3+" element="Tl" mass="204.38" name="tip3pfb_standard-Tl3+"/>
<Type class="tip3pfb_standard-Y3+" element="Y" mass="88.91" name="tip3pfb_standard-Y3+"/>
<Type class="tip3pfb_standard-La3+" element="La" mass="138.91" name="tip3pfb_standard-La3+"/>
<Type class="tip3pfb_standard-Ce3+" element="Ce" mass="140.12" name="tip3pfb_standard-Ce3+"/>
<Type class="tip3pfb_standard-Pr3+" element="Pr" mass="140.91" name="tip3pfb_standard-Pr3+"/>
<Type class="tip3pfb_standard-Nd3+" element="Nd" mass="144.24" name="tip3pfb_standard-Nd3+"/>
<Type class="tip3pfb_standard-Sm3+" element="Sm" mass="150.36" name="tip3pfb_standard-Sm3+"/>
<Type class="tip3pfb_standard-Eu3+" element="Eu" mass="151.96" name="tip3pfb_standard-Eu3+"/>
<Type class="tip3pfb_standard-Gd3+" element="Gd" mass="157.25" name="tip3pfb_standard-Gd3+"/>
<Type class="tip3pfb_standard-Tb3+" element="Tb" mass="158.93" name="tip3pfb_standard-Tb3+"/>
<Type class="tip3pfb_standard-Dy3+" element="Dy" mass="162.5" name="tip3pfb_standard-Dy3+"/>
<Type class="tip3pfb_standard-Er3+" element="Er" mass="167.26" name="tip3pfb_standard-Er3+"/>
<Type class="tip3pfb_standard-Tm3+" element="Tm" mass="168.93" name="tip3pfb_standard-Tm3+"/>
<Type class="tip3pfb_standard-Lu3+" element="Lu" mass="174.97" name="tip3pfb_standard-Lu3+"/>
<Type class="tip3pfb_standard-Hf4+" element="Hf" mass="178.49" name="tip3pfb_standard-Hf4+"/>
<Type class="tip3pfb_standard-Zr4+" element="Zr" mass="91.22" name="tip3pfb_standard-Zr4+"/>
<Type class="tip3pfb_standard-Ce4+" element="Ce" mass="140.12" name="tip3pfb_standard-Ce4+"/>
<Type class="tip3pfb_standard-U4+" element="U" mass="238.03" name="tip3pfb_standard-U4+"/>
<Type class="tip3pfb_standard-Pu4+" element="Pu" mass="244.06" name="tip3pfb_standard-Pu4+"/>
<Type class="tip3pfb_standard-Th4+" element="Th" mass="232.04" name="tip3pfb_standard-Th4+"/>
<Type name="tip3p-fb-O" class="tip3p-fb-O" element="O" mass="15.99943"/>
<Type name="tip3p-fb-H" class="tip3p-fb-H" element="H" mass="1.007947"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip3pfb_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip3pfb_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip3pfb_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip3pfb_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip3pfb_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip3pfb_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip3pfb_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip3pfb_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip3pfb_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip3pfb_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip3pfb_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip3pfb_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip3pfb_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip3pfb_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip3pfb_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip3pfb_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip3pfb_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip3pfb_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip3pfb_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip3pfb_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip3pfb_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip3pfb_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip3pfb_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip3pfb_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip3pfb_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip3pfb_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip3pfb_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip3pfb_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip3pfb_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip3pfb_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip3pfb_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip3pfb_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip3pfb_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip3pfb_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip3pfb_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip3pfb_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip3pfb_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip3pfb_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip3pfb_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip3pfb_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip3pfb_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip3pfb_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip3pfb_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip3pfb_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip3pfb_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip3pfb_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip3pfb_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip3pfb_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip3pfb_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip3pfb_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip3pfb_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip3pfb_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip3pfb_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip3pfb_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip3pfb_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip3pfb_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip3pfb_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip3p-fb-O" charge="-0.848448690103"/>
<Atom name="H1" type="tip3p-fb-H" charge="0.4242243450515"/>
<Atom name="H2" type="tip3p-fb-H" charge="0.4242243450515"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip3p-fb-O" type2="tip3p-fb-H" length="0.101181082494" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip3p-fb-H" type2="tip3p-fb-O" type3="tip3p-fb-H" angle="1.88754640288" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.1171084864" sigma="0.18263423721876956" type="tip3pfb_standard-Li+"/>
<Atom epsilon="0.3658460312" sigma="0.2439280690268249" type="tip3pfb_standard-Na+"/>
<Atom epsilon="0.8103692536" sigma="0.3037964628858557" type="tip3pfb_standard-K+"/>
<Atom epsilon="1.3716068296000001" sigma="0.32303987519768707" type="tip3pfb_standard-Rb+"/>
<Atom epsilon="1.7009608496" sigma="0.3520831734090621" type="tip3pfb_standard-Cs+"/>
<Atom epsilon="0.014074976" sigma="0.4103479495754403" type="tip3pfb_standard-F-"/>
<Atom epsilon="0.14891274399999999" sigma="0.4477656957373345" type="tip3pfb_standard-Cl-"/>
<Atom epsilon="0.24541419360000002" sigma="0.46469277138200105" type="tip3pfb_standard-Br-"/>
<Atom epsilon="0.22460381440000002" sigma="0.5095940667762741" type="tip3pfb_standard-I-"/>
<Atom epsilon="1.6526800000000002e-05" sigma="0.17033983490843285" type="tip3pfb_standard-Be2+"/>
<Atom epsilon="0.00621311448" sigma="0.21702292773898668" type="tip3pfb_standard-Cu2+"/>
<Atom epsilon="0.0109754688" sigma="0.22361557825322517" type="tip3pfb_standard-Ni2+"/>
<Atom epsilon="0.01287174128" sigma="0.22557555543313393" type="tip3pfb_standard-Pt2+"/>
<Atom epsilon="0.01381916624" sigma="0.22646645415127425" type="tip3pfb_standard-Zn2+"/>
<Atom epsilon="0.02024604128" sigma="0.23145548697286014" type="tip3pfb_standard-Co2+"/>
<Atom epsilon="0.021335931440000004" sigma="0.23216820594737242" type="tip3pfb_standard-Pd2+"/>
<Atom epsilon="0.032257342960000004" sigma="0.2380481374870987" type="tip3pfb_standard-Ag2+"/>
<Atom epsilon="0.03632456752" sigma="0.23982993492337937" type="tip3pfb_standard-Cr2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip3pfb_standard-Fe2+"/>
<Atom epsilon="0.042686716080000006" sigma="0.2423244513341723" type="tip3pfb_standard-Mg2+"/>
<Atom epsilon="0.04465579016" sigma="0.24303717030868457" type="tip3pfb_standard-V2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3pfb_standard-Mn2+"/>
<Atom epsilon="0.0705719464" sigma="0.25069889928469147" type="tip3pfb_standard-Hg2+"/>
<Atom epsilon="0.07419972544" sigma="0.2515897980028318" type="tip3pfb_standard-Cd2+"/>
<Atom epsilon="0.426181194" sigma="0.29257113903728743" type="tip3pfb_standard-Yb2+"/>
<Atom epsilon="0.4432056808" sigma="0.29381839724268394" type="tip3pfb_standard-Ca2+"/>
<Atom epsilon="0.48608615792" sigma="0.29684745288436104" type="tip3pfb_standard-Sn2+"/>
<Atom epsilon="0.71203621616" sigma="0.31092365263097843" type="tip3pfb_standard-Pb2+"/>
<Atom epsilon="0.8985523254400001" sigma="0.3210798980177783" type="tip3pfb_standard-Eu2+"/>
<Atom epsilon="0.92601852816" sigma="0.32250533596680286" type="tip3pfb_standard-Sr2+"/>
<Atom epsilon="0.95724882464" sigma="0.32410895365945547" type="tip3pfb_standard-Sm2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3pfb_standard-Ba2+"/>
<Atom epsilon="1.7014071987200001" sigma="0.35974490238506907" type="tip3pfb_standard-Ra2+"/>
<Atom epsilon="0.04721589608000001" sigma="0.2439280690268249" type="tip3pfb_standard-Al3+"/>
<Atom epsilon="0.09989325104" sigma="0.25711337005530194" type="tip3pfb_standard-Fe3+"/>
<Atom epsilon="0.07644268416000001" sigma="0.252124337233716" type="tip3pfb_standard-Cr3+"/>
<Atom epsilon="0.15168878616" sigma="0.2656659977494492" type="tip3pfb_standard-In3+"/>
<Atom epsilon="0.27501557520000003" sigma="0.2799203772396946" type="tip3pfb_standard-Tl3+"/>
<Atom epsilon="0.39786810784" sigma="0.29043298211375057" type="tip3pfb_standard-Y3+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip3pfb_standard-La3+"/>
<Atom epsilon="0.83118754056" sigma="0.31751630314521695" type="tip3pfb_standard-Ce3+"/>
<Atom epsilon="0.8245589130400001" sigma="0.31715994365796085" type="tip3pfb_standard-Pr3+"/>
<Atom epsilon="0.64794725224" sigma="0.307181878014789" type="tip3pfb_standard-Nd3+"/>
<Atom epsilon="0.60967151816" sigma="0.3048655413476241" type="tip3pfb_standard-Sm3+"/>
<Atom epsilon="0.62426246504" sigma="0.3057564400657644" type="tip3pfb_standard-Eu3+"/>
<Atom epsilon="0.46563832232" sigma="0.29542201493533654" type="tip3pfb_standard-Gd3+"/>
<Atom epsilon="0.4991058036" sigma="0.2977383516025014" type="tip3pfb_standard-Tb3+"/>
<Atom epsilon="0.41424963936000003" sigma="0.29168024031914713" type="tip3pfb_standard-Dy3+"/>
<Atom epsilon="0.40953067312" sigma="0.2913238808318909" type="tip3pfb_standard-Er3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip3pfb_standard-Tm3+"/>
<Atom epsilon="0.38639884336" sigma="0.2895420833956103" type="tip3pfb_standard-Lu3+"/>
<Atom epsilon="0.33197918711999996" sigma="0.2850875898049086" type="tip3pfb_standard-Hf4+"/>
<Atom epsilon="0.35100580160000006" sigma="0.28669120749756116" type="tip3pfb_standard-Zr4+"/>
<Atom epsilon="0.77874118424" sigma="0.31466542724716784" type="tip3pfb_standard-Ce4+"/>
<Atom epsilon="0.8646299178400001" sigma="0.31929810058149766" type="tip3pfb_standard-U4+"/>
<Atom epsilon="0.73399083568" sigma="0.3121709108363749" type="tip3pfb_standard-Pu4+"/>
<Atom epsilon="0.7917259353600001" sigma="0.31537814622168014" type="tip3pfb_standard-Th4+"/>
<Atom type="tip3p-fb-O" sigma="0.317796456355" epsilon="0.652143528104"/>
<Atom type="tip3p-fb-H" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/amber19/tip4pew.xml 0 → 100644
View file @ 94e0853a
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip4pew" md5hash="7aa9de49a8df5ebc45f74e1f47d13c2a" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip4pew</Source>
<Source Source="parm/frcmod.ions234lm_126_tip4pew" md5hash="3902b775a0fe5d42cab716a82c183747" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip4pew</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip4pew.xml" md5hash="cb450d015f4c238271cef8825f5ad7bd" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip4pew.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279q13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Horn, H.W., Swope, W.C., Pitera, J.W., Madura, J.D., Dick, T.J., Hura, G.L., and Head-Gordon, T. (2004). Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. The Journal of Chemical Physics 120, 9665-9678.</Reference>
<Reference>Horn, H.W., Swope, W.C., and Pitera, J.W. (2005). Characterization of the TIP4P-Ew water model: Vapor pressure and boiling point. The Journal of Chemical Physics 123, 194504.</Reference>
</Info>
<AtomTypes>
<Type class="tip4pew_standard-Li+" element="Li" mass="6.94" name="tip4pew_standard-Li+"/>
<Type class="tip4pew_standard-Na+" element="Na" mass="22.99" name="tip4pew_standard-Na+"/>
<Type class="tip4pew_standard-K+" element="K" mass="39.1" name="tip4pew_standard-K+"/>
<Type class="tip4pew_standard-Rb+" element="Rb" mass="85.47" name="tip4pew_standard-Rb+"/>
<Type class="tip4pew_standard-Cs+" element="Cs" mass="132.91" name="tip4pew_standard-Cs+"/>
<Type class="tip4pew_standard-F-" element="F" mass="19.0" name="tip4pew_standard-F-"/>
<Type class="tip4pew_standard-Cl-" element="Cl" mass="35.45" name="tip4pew_standard-Cl-"/>
<Type class="tip4pew_standard-Br-" element="Br" mass="79.9" name="tip4pew_standard-Br-"/>
<Type class="tip4pew_standard-I-" element="I" mass="126.9" name="tip4pew_standard-I-"/>
<Type class="tip4pew_standard-Be2+" element="Be" mass="9.01" name="tip4pew_standard-Be2+"/>
<Type class="tip4pew_standard-Cu2+" element="Cu" mass="63.55" name="tip4pew_standard-Cu2+"/>
<Type class="tip4pew_standard-Ni2+" element="Ni" mass="58.69" name="tip4pew_standard-Ni2+"/>
<Type class="tip4pew_standard-Pt2+" element="Pt" mass="195.08" name="tip4pew_standard-Pt2+"/>
<Type class="tip4pew_standard-Zn2+" element="Zn" mass="65.4" name="tip4pew_standard-Zn2+"/>
<Type class="tip4pew_standard-Co2+" element="Co" mass="58.93" name="tip4pew_standard-Co2+"/>
<Type class="tip4pew_standard-Pd2+" element="Pd" mass="106.42" name="tip4pew_standard-Pd2+"/>
<Type class="tip4pew_standard-Ag2+" element="Ag" mass="107.87" name="tip4pew_standard-Ag2+"/>
<Type class="tip4pew_standard-Cr2+" element="Cr" mass="52.0" name="tip4pew_standard-Cr2+"/>
<Type class="tip4pew_standard-Fe2+" element="Fe" mass="55.85" name="tip4pew_standard-Fe2+"/>
<Type class="tip4pew_standard-Mg2+" element="Mg" mass="24.305" name="tip4pew_standard-Mg2+"/>
<Type class="tip4pew_standard-V2+" element="V" mass="50.94" name="tip4pew_standard-V2+"/>
<Type class="tip4pew_standard-Mn2+" element="Mn" mass="54.94" name="tip4pew_standard-Mn2+"/>
<Type class="tip4pew_standard-Hg2+" element="Hg" mass="200.59" name="tip4pew_standard-Hg2+"/>
<Type class="tip4pew_standard-Cd2+" element="Cd" mass="112.41" name="tip4pew_standard-Cd2+"/>
<Type class="tip4pew_standard-Yb2+" element="Yb" mass="173.05" name="tip4pew_standard-Yb2+"/>
<Type class="tip4pew_standard-Ca2+" element="Ca" mass="40.08" name="tip4pew_standard-Ca2+"/>
<Type class="tip4pew_standard-Sn2+" element="Sn" mass="118.71" name="tip4pew_standard-Sn2+"/>
<Type class="tip4pew_standard-Pb2+" element="Pb" mass="207.2" name="tip4pew_standard-Pb2+"/>
<Type class="tip4pew_standard-Eu2+" element="Eu" mass="151.96" name="tip4pew_standard-Eu2+"/>
<Type class="tip4pew_standard-Sr2+" element="Sr" mass="87.62" name="tip4pew_standard-Sr2+"/>
<Type class="tip4pew_standard-Sm2+" element="Sm" mass="150.36" name="tip4pew_standard-Sm2+"/>
<Type class="tip4pew_standard-Ba2+" element="Ba" mass="137.33" name="tip4pew_standard-Ba2+"/>
<Type class="tip4pew_standard-Ra2+" element="Ra" mass="226.03" name="tip4pew_standard-Ra2+"/>
<Type class="tip4pew_standard-Al3+" element="Al" mass="26.98" name="tip4pew_standard-Al3+"/>
<Type class="tip4pew_standard-Fe3+" element="Fe" mass="55.85" name="tip4pew_standard-Fe3+"/>
<Type class="tip4pew_standard-Cr3+" element="Cr" mass="52.0" name="tip4pew_standard-Cr3+"/>
<Type class="tip4pew_standard-In3+" element="In" mass="114.82" name="tip4pew_standard-In3+"/>
<Type class="tip4pew_standard-Tl3+" element="Tl" mass="204.38" name="tip4pew_standard-Tl3+"/>
<Type class="tip4pew_standard-Y3+" element="Y" mass="88.91" name="tip4pew_standard-Y3+"/>
<Type class="tip4pew_standard-La3+" element="La" mass="138.91" name="tip4pew_standard-La3+"/>
<Type class="tip4pew_standard-Ce3+" element="Ce" mass="140.12" name="tip4pew_standard-Ce3+"/>
<Type class="tip4pew_standard-Pr3+" element="Pr" mass="140.91" name="tip4pew_standard-Pr3+"/>
<Type class="tip4pew_standard-Nd3+" element="Nd" mass="144.24" name="tip4pew_standard-Nd3+"/>
<Type class="tip4pew_standard-Sm3+" element="Sm" mass="150.36" name="tip4pew_standard-Sm3+"/>
<Type class="tip4pew_standard-Eu3+" element="Eu" mass="151.96" name="tip4pew_standard-Eu3+"/>
<Type class="tip4pew_standard-Gd3+" element="Gd" mass="157.25" name="tip4pew_standard-Gd3+"/>
<Type class="tip4pew_standard-Tb3+" element="Tb" mass="158.93" name="tip4pew_standard-Tb3+"/>
<Type class="tip4pew_standard-Dy3+" element="Dy" mass="162.5" name="tip4pew_standard-Dy3+"/>
<Type class="tip4pew_standard-Er3+" element="Er" mass="167.26" name="tip4pew_standard-Er3+"/>
<Type class="tip4pew_standard-Tm3+" element="Tm" mass="168.93" name="tip4pew_standard-Tm3+"/>
<Type class="tip4pew_standard-Lu3+" element="Lu" mass="174.97" name="tip4pew_standard-Lu3+"/>
<Type class="tip4pew_standard-Hf4+" element="Hf" mass="178.49" name="tip4pew_standard-Hf4+"/>
<Type class="tip4pew_standard-Zr4+" element="Zr" mass="91.22" name="tip4pew_standard-Zr4+"/>
<Type class="tip4pew_standard-Ce4+" element="Ce" mass="140.12" name="tip4pew_standard-Ce4+"/>
<Type class="tip4pew_standard-U4+" element="U" mass="238.03" name="tip4pew_standard-U4+"/>
<Type class="tip4pew_standard-Pu4+" element="Pu" mass="244.06" name="tip4pew_standard-Pu4+"/>
<Type class="tip4pew_standard-Th4+" element="Th" mass="232.04" name="tip4pew_standard-Th4+"/>
<Type name="tip4pew-O" class="tip4pew-O" element="O" mass="15.99943"/>
<Type name="tip4pew-H" class="tip4pew-H" element="H" mass="1.007947"/>
<Type name="tip4pew-M" class="tip4pew-M" mass="0"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip4pew_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip4pew_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip4pew_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip4pew_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip4pew_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip4pew_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip4pew_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip4pew_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip4pew_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip4pew_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip4pew_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip4pew_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip4pew_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip4pew_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip4pew_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip4pew_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip4pew_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip4pew_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip4pew_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip4pew_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip4pew_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip4pew_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip4pew_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip4pew_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip4pew_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip4pew_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip4pew_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip4pew_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip4pew_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip4pew_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip4pew_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip4pew_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip4pew_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip4pew_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip4pew_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip4pew_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip4pew_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip4pew_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip4pew_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip4pew_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip4pew_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip4pew_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip4pew_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip4pew_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip4pew_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip4pew_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip4pew_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip4pew_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip4pew_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip4pew_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip4pew_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip4pew_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip4pew_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip4pew_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip4pew_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip4pew_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip4pew_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip4pew-O" charge="0"/>
<Atom name="H1" type="tip4pew-H" charge="0.52422"/>
<Atom name="H2" type="tip4pew-H" charge="0.52422"/>
<Atom name="M" type="tip4pew-M" charge="-1.04844"/>
<VirtualSite type="average3" siteName="M" atomName1="O" atomName2="H1" atomName3="H2" weight1="0.786646558" weight2="0.106676721" weight3="0.106676721"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip4pew-O" type2="tip4pew-H" length="0.09572" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip4pew-H" type2="tip4pew-O" type3="tip4pew-H" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.4350874656" sigma="0.14396923285147886" type="tip4pew_standard-Li+"/>
<Atom epsilon="0.7047424999999999" sigma="0.21844836568801118" type="tip4pew_standard-Na+"/>
<Atom epsilon="1.1692819784000001" sigma="0.2833057923686279" type="tip4pew_standard-K+"/>
<Atom epsilon="1.8122970896000001" sigma="0.304509181860368" type="tip4pew_standard-Rb+"/>
<Atom epsilon="1.6503026512" sigma="0.3364033559697921" type="tip4pew_standard-Cs+"/>
<Atom epsilon="0.0065906368" sigma="0.4522201893280362" type="tip4pew_standard-F-"/>
<Atom epsilon="0.048791716" sigma="0.49177609241346726" type="tip4pew_standard-Cl-"/>
<Atom epsilon="0.1270986232" sigma="0.4932015303624918" type="tip4pew_standard-Br-"/>
<Atom epsilon="0.1745071088" sigma="0.5259866031900563" type="tip4pew_standard-I-"/>
<Atom epsilon="4.853439999999999e-06" sigma="0.1635690046505663" type="tip4pew_standard-Be2+"/>
<Atom epsilon="0.00424537928" sigma="0.2129247936355411" type="tip4pew_standard-Cu2+"/>
<Atom epsilon="0.00651925776" sigma="0.21755746696987088" type="tip4pew_standard-Ni2+"/>
<Atom epsilon="0.01034627888" sigma="0.2229028592787129" type="tip4pew_standard-Pt2+"/>
<Atom epsilon="0.01050071032" sigma="0.22308103902234097" type="tip4pew_standard-Zn2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pew_standard-Co2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pew_standard-Pd2+"/>
<Atom epsilon="0.027520218160000002" sigma="0.23573180081993375" type="tip4pew_standard-Ag2+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pew_standard-Cr2+"/>
<Atom epsilon="0.035064095680000004" sigma="0.23929539569249514" type="tip4pew_standard-Fe2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pew_standard-Mg2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pew_standard-V2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pew_standard-Mn2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pew_standard-Hg2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="tip4pew_standard-Cd2+"/>
<Atom epsilon="0.45559312408" sigma="0.29470929596082424" type="tip4pew_standard-Yb2+"/>
<Atom epsilon="0.46311578872000003" sigma="0.29524383519170844" type="tip4pew_standard-Ca2+"/>
<Atom epsilon="0.49648724720000004" sigma="0.29756017185887335" type="tip4pew_standard-Sn2+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip4pew_standard-Pb2+"/>
<Atom epsilon="0.9712365224" sigma="0.3248216726339677" type="tip4pew_standard-Eu2+"/>
<Atom epsilon="0.985288068" sigma="0.32553439160847997" type="tip4pew_standard-Sr2+"/>
<Atom epsilon="1.02424478992" sigma="0.3274943687883887" type="tip4pew_standard-Sm2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pew_standard-Ba2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pew_standard-Ra2+"/>
<Atom epsilon="0.01678206584" sigma="0.22896097056206718" type="tip4pew_standard-Al3+"/>
<Atom epsilon="0.05043699032" sigma="0.2449971474885933" type="tip4pew_standard-Fe3+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pew_standard-Cr3+"/>
<Atom epsilon="0.10650049832000001" sigma="0.2583606282606984" type="tip4pew_standard-In3+"/>
<Atom epsilon="0.16579982824" sigma="0.2676259749293579" type="tip4pew_standard-Tl3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pew_standard-Y3+"/>
<Atom epsilon="0.59811815528" sigma="0.30415282237311186" type="tip4pew_standard-La3+"/>
<Atom epsilon="0.66295839824" sigma="0.3080727767329294" type="tip4pew_standard-Ce3+"/>
<Atom epsilon="0.64198735344" sigma="0.30682551852753287" type="tip4pew_standard-Pr3+"/>
<Atom epsilon="0.49387597096" sigma="0.2973819921152453" type="tip4pew_standard-Nd3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip4pew_standard-Sm3+"/>
<Atom epsilon="0.4580931896" sigma="0.29488747570445234" type="tip4pew_standard-Eu3+"/>
<Atom epsilon="0.35748949536" sigma="0.2872257467284454" type="tip4pew_standard-Gd3+"/>
<Atom epsilon="0.37289213824" sigma="0.28847300493384187" type="tip4pew_standard-Tb3+"/>
<Atom epsilon="0.32577870832" sigma="0.28455305057402436" type="tip4pew_standard-Dy3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pew_standard-Er3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pew_standard-Tm3+"/>
<Atom epsilon="0.28625681168" sigma="0.280989455701463" type="tip4pew_standard-Lu3+"/>
<Atom epsilon="0.14196839183999999" sigma="0.26424055980042466" type="tip4pew_standard-Hf4+"/>
<Atom epsilon="0.16712607256" sigma="0.26780415467298596" type="tip4pew_standard-Zr4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pew_standard-Ce4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pew_standard-U4+"/>
<Atom epsilon="0.43343181496" sigma="0.29310567826817163" type="tip4pew_standard-Pu4+"/>
<Atom epsilon="0.5502288444000001" sigma="0.3011237667314347" type="tip4pew_standard-Th4+"/>
<Atom type="tip4pew-O" sigma="0.316435" epsilon="0.680946"/>
<Atom type="tip4pew-H" sigma="1" epsilon="0"/>
<Atom type="tip4pew-M" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
wrappers/python/openmm/app/data/amber19/tip4pfb.xml 0 → 100644
View file @ 94e0853a
<ForceField>
<Info>
<DateGenerated>2017-11-25</DateGenerated>
<Source Source="parm/frcmod.ionsjc_tip4pew" md5hash="7aa9de49a8df5ebc45f74e1f47d13c2a" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ionsjc_tip4pew</Source>
<Source Source="parm/frcmod.ions234lm_126_tip4pew" md5hash="3902b775a0fe5d42cab716a82c183747" sourcePackage="AmberTools" sourcePackageVersion="17">parm/frcmod.ions234lm_126_tip4pew</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="17">lib/atomic_ions.lib</Source>
<Source Source="tip4pfb.xml" md5hash="5da20fd20f6aefc31c499fc7c635bf69" sourcePackage="OpenMM" sourcePackageVersion="7.2">tip4pfb.xml</Source>
<Reference>Joung, I.S., and Cheatham, Thomas E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 112, 9020-9041.</Reference>
<Reference>Joung, I.S., and Cheatham, T.E. (2009). Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters. J. Phys. Chem. B 113, 13279q13290.</Reference>
<Reference>Li, P., Roberts, B.P., Chakravorty, D.K., and Merz, K.M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. J. Chem. Theory Comput. 9, 2733-2748.</Reference>
<Reference>Lee-Ping Wang, Todd J. Martinez and Vijay S. Pande. (2014). Building force fields - an automatic, systematic and reproducible approach. Journal of Physical Chemistry Letters, 5, 1885-1891.</Reference>
</Info>
<AtomTypes>
<Type class="tip4pfb_standard-Li+" element="Li" mass="6.94" name="tip4pfb_standard-Li+"/>
<Type class="tip4pfb_standard-Na+" element="Na" mass="22.99" name="tip4pfb_standard-Na+"/>
<Type class="tip4pfb_standard-K+" element="K" mass="39.1" name="tip4pfb_standard-K+"/>
<Type class="tip4pfb_standard-Rb+" element="Rb" mass="85.47" name="tip4pfb_standard-Rb+"/>
<Type class="tip4pfb_standard-Cs+" element="Cs" mass="132.91" name="tip4pfb_standard-Cs+"/>
<Type class="tip4pfb_standard-F-" element="F" mass="19.0" name="tip4pfb_standard-F-"/>
<Type class="tip4pfb_standard-Cl-" element="Cl" mass="35.45" name="tip4pfb_standard-Cl-"/>
<Type class="tip4pfb_standard-Br-" element="Br" mass="79.9" name="tip4pfb_standard-Br-"/>
<Type class="tip4pfb_standard-I-" element="I" mass="126.9" name="tip4pfb_standard-I-"/>
<Type class="tip4pfb_standard-Be2+" element="Be" mass="9.01" name="tip4pfb_standard-Be2+"/>
<Type class="tip4pfb_standard-Cu2+" element="Cu" mass="63.55" name="tip4pfb_standard-Cu2+"/>
<Type class="tip4pfb_standard-Ni2+" element="Ni" mass="58.69" name="tip4pfb_standard-Ni2+"/>
<Type class="tip4pfb_standard-Pt2+" element="Pt" mass="195.08" name="tip4pfb_standard-Pt2+"/>
<Type class="tip4pfb_standard-Zn2+" element="Zn" mass="65.4" name="tip4pfb_standard-Zn2+"/>
<Type class="tip4pfb_standard-Co2+" element="Co" mass="58.93" name="tip4pfb_standard-Co2+"/>
<Type class="tip4pfb_standard-Pd2+" element="Pd" mass="106.42" name="tip4pfb_standard-Pd2+"/>
<Type class="tip4pfb_standard-Ag2+" element="Ag" mass="107.87" name="tip4pfb_standard-Ag2+"/>
<Type class="tip4pfb_standard-Cr2+" element="Cr" mass="52.0" name="tip4pfb_standard-Cr2+"/>
<Type class="tip4pfb_standard-Fe2+" element="Fe" mass="55.85" name="tip4pfb_standard-Fe2+"/>
<Type class="tip4pfb_standard-Mg2+" element="Mg" mass="24.305" name="tip4pfb_standard-Mg2+"/>
<Type class="tip4pfb_standard-V2+" element="V" mass="50.94" name="tip4pfb_standard-V2+"/>
<Type class="tip4pfb_standard-Mn2+" element="Mn" mass="54.94" name="tip4pfb_standard-Mn2+"/>
<Type class="tip4pfb_standard-Hg2+" element="Hg" mass="200.59" name="tip4pfb_standard-Hg2+"/>
<Type class="tip4pfb_standard-Cd2+" element="Cd" mass="112.41" name="tip4pfb_standard-Cd2+"/>
<Type class="tip4pfb_standard-Yb2+" element="Yb" mass="173.05" name="tip4pfb_standard-Yb2+"/>
<Type class="tip4pfb_standard-Ca2+" element="Ca" mass="40.08" name="tip4pfb_standard-Ca2+"/>
<Type class="tip4pfb_standard-Sn2+" element="Sn" mass="118.71" name="tip4pfb_standard-Sn2+"/>
<Type class="tip4pfb_standard-Pb2+" element="Pb" mass="207.2" name="tip4pfb_standard-Pb2+"/>
<Type class="tip4pfb_standard-Eu2+" element="Eu" mass="151.96" name="tip4pfb_standard-Eu2+"/>
<Type class="tip4pfb_standard-Sr2+" element="Sr" mass="87.62" name="tip4pfb_standard-Sr2+"/>
<Type class="tip4pfb_standard-Sm2+" element="Sm" mass="150.36" name="tip4pfb_standard-Sm2+"/>
<Type class="tip4pfb_standard-Ba2+" element="Ba" mass="137.33" name="tip4pfb_standard-Ba2+"/>
<Type class="tip4pfb_standard-Ra2+" element="Ra" mass="226.03" name="tip4pfb_standard-Ra2+"/>
<Type class="tip4pfb_standard-Al3+" element="Al" mass="26.98" name="tip4pfb_standard-Al3+"/>
<Type class="tip4pfb_standard-Fe3+" element="Fe" mass="55.85" name="tip4pfb_standard-Fe3+"/>
<Type class="tip4pfb_standard-Cr3+" element="Cr" mass="52.0" name="tip4pfb_standard-Cr3+"/>
<Type class="tip4pfb_standard-In3+" element="In" mass="114.82" name="tip4pfb_standard-In3+"/>
<Type class="tip4pfb_standard-Tl3+" element="Tl" mass="204.38" name="tip4pfb_standard-Tl3+"/>
<Type class="tip4pfb_standard-Y3+" element="Y" mass="88.91" name="tip4pfb_standard-Y3+"/>
<Type class="tip4pfb_standard-La3+" element="La" mass="138.91" name="tip4pfb_standard-La3+"/>
<Type class="tip4pfb_standard-Ce3+" element="Ce" mass="140.12" name="tip4pfb_standard-Ce3+"/>
<Type class="tip4pfb_standard-Pr3+" element="Pr" mass="140.91" name="tip4pfb_standard-Pr3+"/>
<Type class="tip4pfb_standard-Nd3+" element="Nd" mass="144.24" name="tip4pfb_standard-Nd3+"/>
<Type class="tip4pfb_standard-Sm3+" element="Sm" mass="150.36" name="tip4pfb_standard-Sm3+"/>
<Type class="tip4pfb_standard-Eu3+" element="Eu" mass="151.96" name="tip4pfb_standard-Eu3+"/>
<Type class="tip4pfb_standard-Gd3+" element="Gd" mass="157.25" name="tip4pfb_standard-Gd3+"/>
<Type class="tip4pfb_standard-Tb3+" element="Tb" mass="158.93" name="tip4pfb_standard-Tb3+"/>
<Type class="tip4pfb_standard-Dy3+" element="Dy" mass="162.5" name="tip4pfb_standard-Dy3+"/>
<Type class="tip4pfb_standard-Er3+" element="Er" mass="167.26" name="tip4pfb_standard-Er3+"/>
<Type class="tip4pfb_standard-Tm3+" element="Tm" mass="168.93" name="tip4pfb_standard-Tm3+"/>
<Type class="tip4pfb_standard-Lu3+" element="Lu" mass="174.97" name="tip4pfb_standard-Lu3+"/>
<Type class="tip4pfb_standard-Hf4+" element="Hf" mass="178.49" name="tip4pfb_standard-Hf4+"/>
<Type class="tip4pfb_standard-Zr4+" element="Zr" mass="91.22" name="tip4pfb_standard-Zr4+"/>
<Type class="tip4pfb_standard-Ce4+" element="Ce" mass="140.12" name="tip4pfb_standard-Ce4+"/>
<Type class="tip4pfb_standard-U4+" element="U" mass="238.03" name="tip4pfb_standard-U4+"/>
<Type class="tip4pfb_standard-Pu4+" element="Pu" mass="244.06" name="tip4pfb_standard-Pu4+"/>
<Type class="tip4pfb_standard-Th4+" element="Th" mass="232.04" name="tip4pfb_standard-Th4+"/>
<Type name="tip4p-fb-O" class="tip4p-fb-O" element="O" mass="15.99943"/>
<Type name="tip4p-fb-H" class="tip4p-fb-H" element="H" mass="1.007947"/>
<Type name="tip4p-fb-M" class="tip4p-fb-M" mass="0"/>
</AtomTypes>
<Residues>
<Residue name="AL">
<Atom charge="3.0" name="AL" type="tip4pfb_standard-Al3+"/>
</Residue>
<Residue name="Ag">
<Atom charge="2.0" name="Ag" type="tip4pfb_standard-Ag2+"/>
</Residue>
<Residue name="BA">
<Atom charge="2.0" name="BA" type="tip4pfb_standard-Ba2+"/>
</Residue>
<Residue name="BR">
<Atom charge="-1.0" name="BR" type="tip4pfb_standard-Br-"/>
</Residue>
<Residue name="Be">
<Atom charge="2.0" name="Be" type="tip4pfb_standard-Be2+"/>
</Residue>
<Residue name="CA">
<Atom charge="2.0" name="CA" type="tip4pfb_standard-Ca2+"/>
</Residue>
<Residue name="CD">
<Atom charge="2.0" name="CD" type="tip4pfb_standard-Cd2+"/>
</Residue>
<Residue name="CE">
<Atom charge="3.0" name="CE" type="tip4pfb_standard-Ce3+"/>
</Residue>
<Residue name="CL">
<Atom charge="-1.0" name="CL" type="tip4pfb_standard-Cl-"/>
</Residue>
<Residue name="CO">
<Atom charge="2.0" name="CO" type="tip4pfb_standard-Co2+"/>
</Residue>
<Residue name="CR">
<Atom charge="3.0" name="CR" type="tip4pfb_standard-Cr3+"/>
</Residue>
<Residue name="CS">
<Atom charge="1.0" name="CS" type="tip4pfb_standard-Cs+"/>
</Residue>
<Residue name="CU">
<Atom charge="2.0" name="CU" type="tip4pfb_standard-Cu2+"/>
</Residue>
<Residue name="Ce">
<Atom charge="4.0" name="Ce" type="tip4pfb_standard-Ce4+"/>
</Residue>
<Residue name="Cr">
<Atom charge="2.0" name="Cr" type="tip4pfb_standard-Cr2+"/>
</Residue>
<Residue name="Dy">
<Atom charge="3.0" name="Dy" type="tip4pfb_standard-Dy3+"/>
</Residue>
<Residue name="EU">
<Atom charge="2.0" name="EU" type="tip4pfb_standard-Eu2+"/>
</Residue>
<Residue name="EU3">
<Atom charge="3.0" name="EU3" type="tip4pfb_standard-Eu3+"/>
</Residue>
<Residue name="Er">
<Atom charge="3.0" name="Er" type="tip4pfb_standard-Er3+"/>
</Residue>
<Residue name="F">
<Atom charge="-1.0" name="F" type="tip4pfb_standard-F-"/>
</Residue>
<Residue name="FE">
<Atom charge="3.0" name="FE" type="tip4pfb_standard-Fe3+"/>
</Residue>
<Residue name="FE2">
<Atom charge="2.0" name="FE2" type="tip4pfb_standard-Fe2+"/>
</Residue>
<Residue name="GD3">
<Atom charge="3.0" name="GD" type="tip4pfb_standard-Gd3+"/>
</Residue>
<Residue name="HG">
<Atom charge="2.0" name="HG" type="tip4pfb_standard-Hg2+"/>
</Residue>
<Residue name="Hf">
<Atom charge="4.0" name="Hf" type="tip4pfb_standard-Hf4+"/>
</Residue>
<Residue name="IN">
<Atom charge="3.0" name="IN" type="tip4pfb_standard-In3+"/>
</Residue>
<Residue name="IOD">
<Atom charge="-1.0" name="I" type="tip4pfb_standard-I-"/>
</Residue>
<Residue name="K">
<Atom charge="1.0" name="K" type="tip4pfb_standard-K+"/>
</Residue>
<Residue name="LA">
<Atom charge="3.0" name="LA" type="tip4pfb_standard-La3+"/>
</Residue>
<Residue name="LI">
<Atom charge="1.0" name="LI" type="tip4pfb_standard-Li+"/>
</Residue>
<Residue name="LU">
<Atom charge="3.0" name="LU" type="tip4pfb_standard-Lu3+"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="tip4pfb_standard-Mg2+"/>
</Residue>
<Residue name="MN">
<Atom charge="2.0" name="MN" type="tip4pfb_standard-Mn2+"/>
</Residue>
<Residue name="NA">
<Atom charge="1.0" name="NA" type="tip4pfb_standard-Na+"/>
</Residue>
<Residue name="NI">
<Atom charge="2.0" name="NI" type="tip4pfb_standard-Ni2+"/>
</Residue>
<Residue name="Nd">
<Atom charge="3.0" name="Nd" type="tip4pfb_standard-Nd3+"/>
</Residue>
<Residue name="PB">
<Atom charge="2.0" name="PB" type="tip4pfb_standard-Pb2+"/>
</Residue>
<Residue name="PD">
<Atom charge="2.0" name="PD" type="tip4pfb_standard-Pd2+"/>
</Residue>
<Residue name="PR">
<Atom charge="3.0" name="PR" type="tip4pfb_standard-Pr3+"/>
</Residue>
<Residue name="PT">
<Atom charge="2.0" name="PT" type="tip4pfb_standard-Pt2+"/>
</Residue>
<Residue name="Pu">
<Atom charge="4.0" name="Pu" type="tip4pfb_standard-Pu4+"/>
</Residue>
<Residue name="RB">
<Atom charge="1.0" name="RB" type="tip4pfb_standard-Rb+"/>
</Residue>
<Residue name="Ra">
<Atom charge="2.0" name="Ra" type="tip4pfb_standard-Ra2+"/>
</Residue>
<Residue name="SM">
<Atom charge="3.0" name="SM" type="tip4pfb_standard-Sm3+"/>
</Residue>
<Residue name="SR">
<Atom charge="2.0" name="SR" type="tip4pfb_standard-Sr2+"/>
</Residue>
<Residue name="Sm">
<Atom charge="2.0" name="Sm" type="tip4pfb_standard-Sm2+"/>
</Residue>
<Residue name="Sn">
<Atom charge="2.0" name="Sn" type="tip4pfb_standard-Sn2+"/>
</Residue>
<Residue name="TB">
<Atom charge="3.0" name="TB" type="tip4pfb_standard-Tb3+"/>
</Residue>
<Residue name="Th">
<Atom charge="4.0" name="Th" type="tip4pfb_standard-Th4+"/>
</Residue>
<Residue name="Tl">
<Atom charge="3.0" name="Tl" type="tip4pfb_standard-Tl3+"/>
</Residue>
<Residue name="Tm">
<Atom charge="3.0" name="Tm" type="tip4pfb_standard-Tm3+"/>
</Residue>
<Residue name="U4+">
<Atom charge="4.0" name="U" type="tip4pfb_standard-U4+"/>
</Residue>
<Residue name="V2+">
<Atom charge="2.0" name="V2+" type="tip4pfb_standard-V2+"/>
</Residue>
<Residue name="Y">
<Atom charge="3.0" name="Y" type="tip4pfb_standard-Y3+"/>
</Residue>
<Residue name="YB2">
<Atom charge="2.0" name="YB2" type="tip4pfb_standard-Yb2+"/>
</Residue>
<Residue name="ZN">
<Atom charge="2.0" name="ZN" type="tip4pfb_standard-Zn2+"/>
</Residue>
<Residue name="Zr">
<Atom charge="4.0" name="Zr" type="tip4pfb_standard-Zr4+"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="tip4p-fb-O" charge="0"/>
<Atom name="H1" type="tip4p-fb-H" charge="5.258681106763e-01"/>
<Atom name="H2" type="tip4p-fb-H" charge="5.258681106763e-01"/>
<Atom name="M" type="tip4p-fb-M" charge="-1.0517362213526e+00"/>
<VirtualSite type="average3" index="3" atom1="0" atom2="1" atom3="2" weight1="8.203146574531e-01" weight2="8.984267127345e-02" weight3="8.984267127345e-02"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="tip4p-fb-O" type2="tip4p-fb-H" length="0.09572" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="tip4p-fb-H" type2="tip4p-fb-O" type3="tip4p-fb-H" angle="1.82421813418" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.4350874656" sigma="0.14396923285147886" type="tip4pfb_standard-Li+"/>
<Atom epsilon="0.7047424999999999" sigma="0.21844836568801118" type="tip4pfb_standard-Na+"/>
<Atom epsilon="1.1692819784000001" sigma="0.2833057923686279" type="tip4pfb_standard-K+"/>
<Atom epsilon="1.8122970896000001" sigma="0.304509181860368" type="tip4pfb_standard-Rb+"/>
<Atom epsilon="1.6503026512" sigma="0.3364033559697921" type="tip4pfb_standard-Cs+"/>
<Atom epsilon="0.0065906368" sigma="0.4522201893280362" type="tip4pfb_standard-F-"/>
<Atom epsilon="0.048791716" sigma="0.49177609241346726" type="tip4pfb_standard-Cl-"/>
<Atom epsilon="0.1270986232" sigma="0.4932015303624918" type="tip4pfb_standard-Br-"/>
<Atom epsilon="0.1745071088" sigma="0.5259866031900563" type="tip4pfb_standard-I-"/>
<Atom epsilon="4.853439999999999e-06" sigma="0.1635690046505663" type="tip4pfb_standard-Be2+"/>
<Atom epsilon="0.00424537928" sigma="0.2129247936355411" type="tip4pfb_standard-Cu2+"/>
<Atom epsilon="0.00651925776" sigma="0.21755746696987088" type="tip4pfb_standard-Ni2+"/>
<Atom epsilon="0.01034627888" sigma="0.2229028592787129" type="tip4pfb_standard-Pt2+"/>
<Atom epsilon="0.01050071032" sigma="0.22308103902234097" type="tip4pfb_standard-Zn2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pfb_standard-Co2+"/>
<Atom epsilon="0.01748020808" sigma="0.2294955097929514" type="tip4pfb_standard-Pd2+"/>
<Atom epsilon="0.027520218160000002" sigma="0.23573180081993375" type="tip4pfb_standard-Ag2+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pfb_standard-Cr2+"/>
<Atom epsilon="0.035064095680000004" sigma="0.23929539569249514" type="tip4pfb_standard-Fe2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pfb_standard-Mg2+"/>
<Atom epsilon="0.03940482832" sigma="0.24107719312877582" type="tip4pfb_standard-V2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pfb_standard-Mn2+"/>
<Atom epsilon="0.06639731856" sigma="0.24962982082292307" type="tip4pfb_standard-Hg2+"/>
<Atom epsilon="0.0698627584" sigma="0.2505207195410634" type="tip4pfb_standard-Cd2+"/>
<Atom epsilon="0.45559312408" sigma="0.29470929596082424" type="tip4pfb_standard-Yb2+"/>
<Atom epsilon="0.46311578872000003" sigma="0.29524383519170844" type="tip4pfb_standard-Ca2+"/>
<Atom epsilon="0.49648724720000004" sigma="0.29756017185887335" type="tip4pfb_standard-Sn2+"/>
<Atom epsilon="0.7530346464" sigma="0.3132399892981433" type="tip4pfb_standard-Pb2+"/>
<Atom epsilon="0.9712365224" sigma="0.3248216726339677" type="tip4pfb_standard-Eu2+"/>
<Atom epsilon="0.985288068" sigma="0.32553439160847997" type="tip4pfb_standard-Sr2+"/>
<Atom epsilon="1.02424478992" sigma="0.3274943687883887" type="tip4pfb_standard-Sm2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pfb_standard-Ba2+"/>
<Atom epsilon="1.8181297948000001" sigma="0.3652684744375391" type="tip4pfb_standard-Ra2+"/>
<Atom epsilon="0.01678206584" sigma="0.22896097056206718" type="tip4pfb_standard-Al3+"/>
<Atom epsilon="0.05043699032" sigma="0.2449971474885933" type="tip4pfb_standard-Fe3+"/>
<Atom epsilon="0.03111050856" sigma="0.23751359825621443" type="tip4pfb_standard-Cr3+"/>
<Atom epsilon="0.10650049832000001" sigma="0.2583606282606984" type="tip4pfb_standard-In3+"/>
<Atom epsilon="0.16579982824" sigma="0.2676259749293579" type="tip4pfb_standard-Tl3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Y3+"/>
<Atom epsilon="0.59811815528" sigma="0.30415282237311186" type="tip4pfb_standard-La3+"/>
<Atom epsilon="0.66295839824" sigma="0.3080727767329294" type="tip4pfb_standard-Ce3+"/>
<Atom epsilon="0.64198735344" sigma="0.30682551852753287" type="tip4pfb_standard-Pr3+"/>
<Atom epsilon="0.49387597096" sigma="0.2973819921152453" type="tip4pfb_standard-Nd3+"/>
<Atom epsilon="0.43830358088" sigma="0.29346203775542773" type="tip4pfb_standard-Sm3+"/>
<Atom epsilon="0.4580931896" sigma="0.29488747570445234" type="tip4pfb_standard-Eu3+"/>
<Atom epsilon="0.35748949536" sigma="0.2872257467284454" type="tip4pfb_standard-Gd3+"/>
<Atom epsilon="0.37289213824" sigma="0.28847300493384187" type="tip4pfb_standard-Tb3+"/>
<Atom epsilon="0.32577870832" sigma="0.28455305057402436" type="tip4pfb_standard-Dy3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Er3+"/>
<Atom epsilon="0.31158691504" sigma="0.2833057923686279" type="tip4pfb_standard-Tm3+"/>
<Atom epsilon="0.28625681168" sigma="0.280989455701463" type="tip4pfb_standard-Lu3+"/>
<Atom epsilon="0.14196839183999999" sigma="0.26424055980042466" type="tip4pfb_standard-Hf4+"/>
<Atom epsilon="0.16712607256" sigma="0.26780415467298596" type="tip4pfb_standard-Zr4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pfb_standard-Ce4+"/>
<Atom epsilon="0.48867542632000005" sigma="0.29702563262798914" type="tip4pfb_standard-U4+"/>
<Atom epsilon="0.43343181496" sigma="0.29310567826817163" type="tip4pfb_standard-Pu4+"/>
<Atom epsilon="0.5502288444000001" sigma="0.3011237667314347" type="tip4pfb_standard-Th4+"/>
<Atom type="tip4p-fb-O" sigma="3.165552430462e-01" epsilon="7.492790213533e-01"/>
<Atom type="tip4p-fb-H" sigma="1" epsilon="0"/>
<Atom type="tip4p-fb-M" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
\ No newline at end of file
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