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Unverified Commit ec580215 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1942 from peastman/ff 

Added new Amber and CHARMM force fields
parents 2eb2c464 9d9a3f4f
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wrappers/python/simtk/openmm/app/data/charmm36/tip4p2005.xml 0 → 100644
View file @ ec580215
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip4p_2005.str" md5hash="78828666bfb4ab391baf9fac0e5c3442" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip4p_2005.str</Source>
<Reference Reference="J.L.F. Abascal and C. Vega. A general purpose model for the condensed phases of water: TIP4P/2005 J. Chem. Phys. 123:234505, 2005." forcefield="tip4p-2005">J.L.F. Abascal and C. Vega. A general purpose model for the condensed phases of water: TIP4P/2005 J. Chem. Phys. 123:234505, 2005.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']" forcefield="ions" type="zinc">['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']</Reference>
</Info>
<AtomTypes>
<Type class="HT" element="H" mass="1.008" name="HT"/>
<Type class="HX" element="H" mass="1.008" name="HX"/>
<Type class="OT" element="O" mass="15.9994" name="OT"/>
<Type class="OX" element="O" mass="15.9994" name="OX"/>
<Type class="LIT" element="Li" mass="6.941" name="LIT"/>
<Type class="SOD" element="Na" mass="22.98977" name="SOD"/>
<Type class="MG" element="Mg" mass="24.305" name="MG"/>
<Type class="POT" element="K" mass="39.0983" name="POT"/>
<Type class="CAL" element="Ca" mass="40.08" name="CAL"/>
<Type class="RUB" element="Rb" mass="85.4678" name="RUB"/>
<Type class="CES" element="Cs" mass="132.90545" name="CES"/>
<Type class="BAR" element="Ba" mass="137.327" name="BAR"/>
<Type class="ZN" element="Zn" mass="65.37" name="ZN"/>
<Type class="CAD" element="Cd" mass="112.411" name="CAD"/>
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
<Type class="LP" mass="0.0" name="LP"/>
</AtomTypes>
<Residues>
<Residue name="TP45">
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<Atom charge="-1.1128" name="OM" type="LP"/>
<Atom charge="0.5564" name="H1" type="HT"/>
<Atom charge="0.5564" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
<Bond atomName1="OH2" atomName2="OM"/>
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/>
<Atom charge="0.32" name="H1" type="HX"/>
<Bond atomName1="O1" atomName2="H1"/>
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT"/>
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG"/>
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL"/>
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB"/>
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES"/>
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR"/>
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<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN"/>
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<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CAD"/>
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond k="0.0" length="0.15139000000000002" type1="HT" type2="HT"/>
<Bond k="376559.99999999994" length="0.09572000000000001" type1="HT" type2="OT"/>
<Bond k="456055.99999999994" length="0.097" type1="OX" type2="HX"/>
<Bond k="0.0" length="0.015" type1="OT" type2="LP"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" k="460.24" type1="HT" type2="OT" type3="HT"/>
</HarmonicAngleForce>
<!--Urey-Bradley terms-->
<AmoebaUreyBradleyForce/>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
<Atom epsilon="0.0" sigma="1.0" type="HX"/>
<Atom epsilon="0.0" sigma="1.0" type="OT"/>
<Atom epsilon="0.0" sigma="1.0" type="OX"/>
<Atom epsilon="0.0" sigma="1.0" type="LIT"/>
<Atom epsilon="0.0" sigma="1.0" type="SOD"/>
<Atom epsilon="0.0" sigma="1.0" type="MG"/>
<Atom epsilon="0.0" sigma="1.0" type="POT"/>
<Atom epsilon="0.0" sigma="1.0" type="CAL"/>
<Atom epsilon="0.0" sigma="1.0" type="RUB"/>
<Atom epsilon="0.0" sigma="1.0" type="CES"/>
<Atom epsilon="0.0" sigma="1.0" type="BAR"/>
<Atom epsilon="0.0" sigma="1.0" type="ZN"/>
<Atom epsilon="0.0" sigma="1.0" type="CAD"/>
<Atom epsilon="0.0" sigma="1.0" type="CLA"/>
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<LennardJonesForce lj14scale="1.0">
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HX"/>
<Atom epsilon="0.7748768" sigma="0.3158414135551131" type="OT"/>
<Atom epsilon="0.50208" sigma="0.30290556416771536" type="OX"/>
<Atom epsilon="0.00974872" sigma="0.23118821735741807" type="LIT"/>
<Atom epsilon="0.1962296" sigma="0.2513670733232967" type="SOD"/>
<Atom epsilon="0.06276" sigma="0.2111429961992604" type="MG"/>
<Atom epsilon="0.364008" sigma="0.3142645228240047" type="POT"/>
<Atom epsilon="0.50208" sigma="0.24357170953956878" type="CAL"/>
<Atom epsilon="0.6276" sigma="0.3385415128933289" type="RUB"/>
<Atom epsilon="0.79496" sigma="0.37417746161894255" type="CES"/>
<Atom epsilon="0.6276" sigma="0.33675971545704825" type="BAR"/>
<Atom epsilon="1.046" sigma="0.194215920554594" type="ZN"/>
<Atom epsilon="0.50208" sigma="0.2417899121032881" type="CAD"/>
<Atom epsilon="0.6276" sigma="0.4044680180357141" type="CLA"/>
<Atom epsilon="0.0" sigma="1.0" type="LP"/>
<NBFixPair epsilon="0.35093300000000005" sigma="0.3323943117381606" type1="CLA" type2="SOD"/>
<NBFixPair epsilon="0.477963424" sigma="0.3635757668730725" type1="CLA" type2="POT"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OCL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/charmm36/tip4pew.xml 0 → 100644
View file @ ec580215
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip4p_ew.str" md5hash="3f17eb8b2a25e79b52d300ee6b41f847" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip4p_ew.str</Source>
<Reference Reference="H.W. Horn; W.C Swope; J.W. Pitera; J.D. Madura; T.J. Dick; G.L. Hura; T. Head-Gordon. J. Chem. Phys. 120:9665-9678, 2004." forcefield="tip4p-ew">H.W. Horn; W.C Swope; J.W. Pitera; J.D. Madura; T.J. Dick; G.L. Hura; T. Head-Gordon. J. Chem. Phys. 120:9665-9678, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']" forcefield="ions" type="zinc">['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']</Reference>
</Info>
<AtomTypes>
<Type class="HT" element="H" mass="1.008" name="HT"/>
<Type class="HX" element="H" mass="1.008" name="HX"/>
<Type class="OT" element="O" mass="15.9994" name="OT"/>
<Type class="OX" element="O" mass="15.9994" name="OX"/>
<Type class="LIT" element="Li" mass="6.941" name="LIT"/>
<Type class="SOD" element="Na" mass="22.98977" name="SOD"/>
<Type class="MG" element="Mg" mass="24.305" name="MG"/>
<Type class="POT" element="K" mass="39.0983" name="POT"/>
<Type class="CAL" element="Ca" mass="40.08" name="CAL"/>
<Type class="RUB" element="Rb" mass="85.4678" name="RUB"/>
<Type class="CES" element="Cs" mass="132.90545" name="CES"/>
<Type class="BAR" element="Ba" mass="137.327" name="BAR"/>
<Type class="ZN" element="Zn" mass="65.37" name="ZN"/>
<Type class="CAD" element="Cd" mass="112.411" name="CAD"/>
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
<Type class="LP" mass="0.0" name="LP"/>
</AtomTypes>
<Residues>
<Residue name="TP4E">
<Atom charge="0.0" name="OH2" type="OT"/>
<Atom charge="-1.04844" name="OM" type="LP"/>
<Atom charge="0.52422" name="H1" type="HT"/>
<Atom charge="0.52422" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
<Bond atomName1="OH2" atomName2="OM"/>
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/>
<Atom charge="0.32" name="H1" type="HX"/>
<Bond atomName1="O1" atomName2="H1"/>
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT"/>
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG"/>
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL"/>
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB"/>
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<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES"/>
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<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN"/>
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<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CAD"/>
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<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA"/>
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<HarmonicBondForce>
<Bond k="0.0" length="0.15139000000000002" type1="HT" type2="HT"/>
<Bond k="376559.99999999994" length="0.09572000000000001" type1="HT" type2="OT"/>
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<Angle angle="1.8242181341844732" k="460.24" type1="HT" type2="OT" type3="HT"/>
</HarmonicAngleForce>
<!--Urey-Bradley terms-->
<AmoebaUreyBradleyForce/>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
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<Atom epsilon="0.6276" sigma="0.4044680180357141" type="CLA"/>
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<NBFixPair epsilon="0.35093300000000005" sigma="0.3323943117381606" type1="CLA" type2="SOD"/>
<NBFixPair epsilon="0.477963424" sigma="0.3635757668730725" type1="CLA" type2="POT"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OCL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/charmm36/tip5p.xml 0 → 100644
View file @ ec580215
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip5p.str" md5hash="4fe0864ddee5e5328419c7dd48b499b2" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip5p.str</Source>
<Reference Reference="M.W. Mahoney and W.L. Jorgensen. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem Phys. 112:8910-8922, 2000." forcefield="tip5p">M.W. Mahoney and W.L. Jorgensen. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem Phys. 112:8910-8922, 2000.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']" forcefield="ions" type="zinc">['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']</Reference>
</Info>
<AtomTypes>
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<Type class="HX" element="H" mass="1.008" name="HX"/>
<Type class="OT" element="O" mass="15.9994" name="OT"/>
<Type class="OX" element="O" mass="15.9994" name="OX"/>
<Type class="LIT" element="Li" mass="6.941" name="LIT"/>
<Type class="SOD" element="Na" mass="22.98977" name="SOD"/>
<Type class="MG" element="Mg" mass="24.305" name="MG"/>
<Type class="POT" element="K" mass="39.0983" name="POT"/>
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<Bond atomName1="O1" atomName2="H1"/>
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<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL"/>
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<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB"/>
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES"/>
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<Residue name="BAR">
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<Bond k="456055.99999999994" length="0.097" type1="OX" type2="HX"/>
<Bond k="0.0" length="0.06999999999999999" type1="OT" type2="LP"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" k="460.24" type1="HT" type2="OT" type3="HT"/>
</HarmonicAngleForce>
<!--Urey-Bradley terms-->
<AmoebaUreyBradleyForce/>
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<Atom epsilon="0.0" sigma="1.0" type="CES"/>
<Atom epsilon="0.0" sigma="1.0" type="BAR"/>
<Atom epsilon="0.0" sigma="1.0" type="ZN"/>
<Atom epsilon="0.0" sigma="1.0" type="CAD"/>
<Atom epsilon="0.0" sigma="1.0" type="CLA"/>
<Atom epsilon="0.0" sigma="1.0" type="LP"/>
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HX"/>
<Atom epsilon="0.66944" sigma="0.3119570951440212" type="OT"/>
<Atom epsilon="0.50208" sigma="0.30290556416771536" type="OX"/>
<Atom epsilon="0.00974872" sigma="0.23118821735741807" type="LIT"/>
<Atom epsilon="0.1962296" sigma="0.2513670733232967" type="SOD"/>
<Atom epsilon="0.06276" sigma="0.2111429961992604" type="MG"/>
<Atom epsilon="0.364008" sigma="0.3142645228240047" type="POT"/>
<Atom epsilon="0.50208" sigma="0.24357170953956878" type="CAL"/>
<Atom epsilon="0.6276" sigma="0.3385415128933289" type="RUB"/>
<Atom epsilon="0.79496" sigma="0.37417746161894255" type="CES"/>
<Atom epsilon="0.6276" sigma="0.33675971545704825" type="BAR"/>
<Atom epsilon="1.046" sigma="0.194215920554594" type="ZN"/>
<Atom epsilon="0.50208" sigma="0.2417899121032881" type="CAD"/>
<Atom epsilon="0.6276" sigma="0.4044680180357141" type="CLA"/>
<Atom epsilon="0.0" sigma="1.0" type="LP"/>
<NBFixPair epsilon="0.35093300000000005" sigma="0.3323943117381606" type1="CLA" type2="SOD"/>
<NBFixPair epsilon="0.477963424" sigma="0.3635757668730725" type1="CLA" type2="POT"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OCL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/charmm36/tip5pew.xml 0 → 100644
View file @ ec580215
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip5p_ew.str" md5hash="a632f2616c2d3d500b76696074f9527c" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip5p_ew.str</Source>
<Reference Reference="Rick, S.W. A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. J Chem Phys 120: 6085-93, 2004." forcefield="tip5p-ew">Rick, S.W. A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. J Chem Phys 120: 6085-93, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']" forcefield="ions" type="zinc">['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']</Reference>
</Info>
<AtomTypes>
<Type class="HT" element="H" mass="1.008" name="HT"/>
<Type class="HX" element="H" mass="1.008" name="HX"/>
<Type class="OT" element="O" mass="15.9994" name="OT"/>
<Type class="OX" element="O" mass="15.9994" name="OX"/>
<Type class="LIT" element="Li" mass="6.941" name="LIT"/>
<Type class="SOD" element="Na" mass="22.98977" name="SOD"/>
<Type class="MG" element="Mg" mass="24.305" name="MG"/>
<Type class="POT" element="K" mass="39.0983" name="POT"/>
<Type class="CAL" element="Ca" mass="40.08" name="CAL"/>
<Type class="RUB" element="Rb" mass="85.4678" name="RUB"/>
<Type class="CES" element="Cs" mass="132.90545" name="CES"/>
<Type class="BAR" element="Ba" mass="137.327" name="BAR"/>
<Type class="ZN" element="Zn" mass="65.37" name="ZN"/>
<Type class="CAD" element="Cd" mass="112.411" name="CAD"/>
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
<Type class="LP" mass="0.0" name="LP"/>
</AtomTypes>
<Residues>
<Residue name="TP5E">
<Atom charge="0.0" name="OH2" type="OT"/>
<Atom charge="0.241" name="H1" type="HT"/>
<Atom charge="0.241" name="H2" type="HT"/>
<Atom charge="-0.241" name="LP1" type="LP"/>
<Atom charge="-0.241" name="LP2" type="LP"/>
<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
<Bond atomName1="OH2" atomName2="LP1"/>
<Bond atomName1="OH2" atomName2="LP2"/>
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/>
<Atom charge="0.32" name="H1" type="HX"/>
<Bond atomName1="O1" atomName2="H1"/>
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT"/>
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG"/>
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL"/>
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB"/>
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES"/>
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR"/>
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN"/>
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CAD"/>
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond k="0.0" length="0.15139000000000002" type1="HT" type2="HT"/>
<Bond k="376559.99999999994" length="0.09572000000000001" type1="HT" type2="OT"/>
<Bond k="456055.99999999994" length="0.097" type1="OX" type2="HX"/>
<Bond k="0.0" length="0.06999999999999999" type1="OT" type2="LP"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" k="460.24" type1="HT" type2="OT" type3="HT"/>
</HarmonicAngleForce>
<!--Urey-Bradley terms-->
<AmoebaUreyBradleyForce/>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
<Atom epsilon="0.0" sigma="1.0" type="HX"/>
<Atom epsilon="0.0" sigma="1.0" type="OT"/>
<Atom epsilon="0.0" sigma="1.0" type="OX"/>
<Atom epsilon="0.0" sigma="1.0" type="LIT"/>
<Atom epsilon="0.0" sigma="1.0" type="SOD"/>
<Atom epsilon="0.0" sigma="1.0" type="MG"/>
<Atom epsilon="0.0" sigma="1.0" type="POT"/>
<Atom epsilon="0.0" sigma="1.0" type="CAL"/>
<Atom epsilon="0.0" sigma="1.0" type="RUB"/>
<Atom epsilon="0.0" sigma="1.0" type="CES"/>
<Atom epsilon="0.0" sigma="1.0" type="BAR"/>
<Atom epsilon="0.0" sigma="1.0" type="ZN"/>
<Atom epsilon="0.0" sigma="1.0" type="CAD"/>
<Atom epsilon="0.0" sigma="1.0" type="CLA"/>
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</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HX"/>
<Atom epsilon="0.680946" sigma="0.30965857645121914" type="OT"/>
<Atom epsilon="0.50208" sigma="0.30290556416771536" type="OX"/>
<Atom epsilon="0.00974872" sigma="0.23118821735741807" type="LIT"/>
<Atom epsilon="0.1962296" sigma="0.2513670733232967" type="SOD"/>
<Atom epsilon="0.06276" sigma="0.2111429961992604" type="MG"/>
<Atom epsilon="0.364008" sigma="0.3142645228240047" type="POT"/>
<Atom epsilon="0.50208" sigma="0.24357170953956878" type="CAL"/>
<Atom epsilon="0.6276" sigma="0.3385415128933289" type="RUB"/>
<Atom epsilon="0.79496" sigma="0.37417746161894255" type="CES"/>
<Atom epsilon="0.6276" sigma="0.33675971545704825" type="BAR"/>
<Atom epsilon="1.046" sigma="0.194215920554594" type="ZN"/>
<Atom epsilon="0.50208" sigma="0.2417899121032881" type="CAD"/>
<Atom epsilon="0.6276" sigma="0.4044680180357141" type="CLA"/>
<Atom epsilon="0.0" sigma="1.0" type="LP"/>
<NBFixPair epsilon="0.35093300000000005" sigma="0.3323943117381606" type1="CLA" type2="SOD"/>
<NBFixPair epsilon="0.477963424" sigma="0.3635757668730725" type1="CLA" type2="POT"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OCL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28419669108676826" type1="OG2D2" type2="SOD"/>
</LennardJonesForce>
</ForceField>
wrappers/python/simtk/openmm/app/data/charmm36/water.xml 0 → 100644
View file @ ec580215
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
<Source Source="toppar/toppar_water_ions.str" md5hash="f59e96950d55df9ca4f9b2d1486d7f4f" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/toppar_water_ions.str</Source>
<Reference Reference="W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; &quot;Comparison of simple potential functions for simulating liquid water&quot;, J. Chem. Phys. 79 926-935 (1983)." forcefield="tip3p">W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey; M.L. Klein; "Comparison of simple potential functions for simulating liquid water", J. Chem. Phys. 79 926-935 (1983).</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference>
<Reference Reference="['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']" forcefield="ions" type="zinc">['Stote, R.H. and Karplus, M. Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: Structure, Function, and Genetics 23:12-31 (1995)']</Reference>
<Reference Reference="['Won, Y., &quot;Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential,&quot; Journal of Physical Chemistry A., 116: 11763-11767, 2012.']" forcefield="ions" type="cations">['Won, Y., "Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential," Journal of Physical Chemistry A., 116: 11763-11767, 2012.']</Reference>
</Info>
<AtomTypes>
<Type class="HT" element="H" mass="1.008" name="HT"/>
<Type class="HX" element="H" mass="1.008" name="HX"/>
<Type class="OT" element="O" mass="15.9994" name="OT"/>
<Type class="OX" element="O" mass="15.9994" name="OX"/>
<Type class="LIT" element="Li" mass="6.941" name="LIT"/>
<Type class="SOD" element="Na" mass="22.98977" name="SOD"/>
<Type class="MG" element="Mg" mass="24.305" name="MG"/>
<Type class="POT" element="K" mass="39.0983" name="POT"/>
<Type class="CAL" element="Ca" mass="40.08" name="CAL"/>
<Type class="RUB" element="Rb" mass="85.4678" name="RUB"/>
<Type class="CES" element="Cs" mass="132.90545" name="CES"/>
<Type class="BAR" element="Ba" mass="137.327" name="BAR"/>
<Type class="ZN" element="Zn" mass="65.37" name="ZN"/>
<Type class="CAD" element="Cd" mass="112.411" name="CAD"/>
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
</AtomTypes>
<Residues>
<Residue name="TIP3">
<Atom charge="-0.834" name="OH2" type="OT"/>
<Atom charge="0.417" name="H1" type="HT"/>
<Atom charge="0.417" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
</Residue>
<Residue name="TP3M">
<Atom charge="-0.834" name="OH2" type="OT"/>
<Atom charge="0.417" name="H1" type="HT"/>
<Atom charge="0.417" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
</Residue>
<Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/>
<Atom charge="0.32" name="H1" type="HX"/>
<Bond atomName1="O1" atomName2="H1"/>
</Residue>
<Residue name="LIT">
<Atom charge="1.0" name="LIT" type="LIT"/>
</Residue>
<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD"/>
</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG"/>
</Residue>
<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
<Atom charge="2.0" name="CAL" type="CAL"/>
</Residue>
<Residue name="RUB">
<Atom charge="1.0" name="RUB" type="RUB"/>
</Residue>
<Residue name="CES">
<Atom charge="1.0" name="CES" type="CES"/>
</Residue>
<Residue name="BAR">
<Atom charge="2.0" name="BAR" type="BAR"/>
</Residue>
<Residue name="ZN2">
<Atom charge="2.0" name="ZN" type="ZN"/>
</Residue>
<Residue name="CD2">
<Atom charge="2.0" name="CD" type="CAD"/>
</Residue>
<Residue name="CLA">
<Atom charge="-1.0" name="CLA" type="CLA"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond k="0.0" length="0.15139000000000002" type1="HT" type2="HT"/>
<Bond k="376559.99999999994" length="0.09572000000000001" type1="HT" type2="OT"/>
<Bond k="456055.99999999994" length="0.097" type1="OX" type2="HX"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle angle="1.8242181341844732" k="460.24" type1="HT" type2="OT" type3="HT"/>
</HarmonicAngleForce>
<!--Urey-Bradley terms-->
<AmoebaUreyBradleyForce/>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<UseAttributeFromResidue name="charge"/>
<Atom epsilon="0.0" sigma="1.0" type="HT"/>
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<Atom epsilon="0.0" sigma="1.0" type="OT"/>
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<Atom epsilon="0.0" sigma="1.0" type="MG"/>
<Atom epsilon="0.0" sigma="1.0" type="POT"/>
<Atom epsilon="0.0" sigma="1.0" type="CAL"/>
<Atom epsilon="0.0" sigma="1.0" type="RUB"/>
<Atom epsilon="0.0" sigma="1.0" type="CES"/>
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<Atom epsilon="0.0" sigma="1.0" type="CAD"/>
<Atom epsilon="0.0" sigma="1.0" type="CLA"/>
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
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<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HX"/>
<Atom epsilon="0.6363864000000001" sigma="0.3150574226831496" type="OT"/>
<Atom epsilon="0.50208" sigma="0.30290556416771536" type="OX"/>
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<Atom epsilon="0.1962296" sigma="0.2513670733232967" type="SOD"/>
<Atom epsilon="0.06276" sigma="0.2111429961992604" type="MG"/>
<Atom epsilon="0.364008" sigma="0.3142645228240047" type="POT"/>
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<NBFixPair epsilon="0.31388368000000005" sigma="0.2877602859593296" type1="OC" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.2788512987779262" type1="OS" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.2877602859593296" type1="OCL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.2788512987779262" type1="OBL" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28152399493234725" type1="O2L" type2="SOD"/>
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<NBFixPair epsilon="0.31388368000000005" sigma="0.28152399493234725" type1="OG2P1" type2="SOD"/>
</LennardJonesForce>
</ForceField>
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