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Commit 65920c60 authored by peastman's avatar peastman
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Merge branch 'master' into membrane

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wrappers/python/simtk/openmm/app/data/charmm36/tip3p-pme-f.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
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<Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-f">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference>
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wrappers/python/simtk/openmm/app/data/charmm36/tip4p2005.xml 0 → 100644
View file @ 65920c60
<ForceField>
<Info>
<DateGenerated>2017-11-26</DateGenerated>
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<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>
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wrappers/python/simtk/openmm/app/data/charmm36/tip4pew.xml 0 → 100644
View file @ 65920c60
<ForceField>
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<Atom epsilon="0.00974872" sigma="0.23118821735741807" type="LIT"/>
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<Atom epsilon="0.06276" sigma="0.2111429961992604" type="MG"/>
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<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"/>
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<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/tip5p.xml 0 → 100644
View file @ 65920c60
<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>
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<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"/>
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<Bond atomName1="OH2" atomName2="LP2"/>
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<Residue name="OH">
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<Bond atomName1="O1" atomName2="H1"/>
</Residue>
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<Atom charge="1.0" name="LIT" type="LIT"/>
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<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"/>
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<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"/>
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<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"/>
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<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"/>
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<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">
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<Atom epsilon="0.00974872" sigma="0.23118821735741807" type="LIT"/>
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<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 @ 65920c60
<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"/>
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<Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/>
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<Bond atomName1="OH2" atomName2="LP1"/>
<Bond atomName1="OH2" atomName2="LP2"/>
</Residue>
<Residue name="OH">
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<Bond atomName1="O1" atomName2="H1"/>
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<Residue name="LIT">
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</Residue>
<Residue name="SOD">
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</Residue>
<Residue name="MG">
<Atom charge="2.0" name="MG" type="MG"/>
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<Residue name="POT">
<Atom charge="1.0" name="POT" type="POT"/>
</Residue>
<Residue name="CAL">
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</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">
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</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"/>
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<Atom epsilon="0.0" sigma="1.0" type="SOD"/>
<Atom epsilon="0.0" sigma="1.0" type="MG"/>
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<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">
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<Atom epsilon="0.6276" sigma="0.3385415128933289" type="RUB"/>
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<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"/>
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</ForceField>
wrappers/python/simtk/openmm/app/data/charmm36/water.xml 0 → 100644
View file @ 65920c60
<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"/>
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<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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<Type class="CES" element="Cs" mass="132.90545" name="CES"/>
<Type class="BAR" element="Ba" mass="137.327" name="BAR"/>
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<Type class="CAD" element="Cd" mass="112.411" name="CAD"/>
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
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<Residues>
<Residue name="TIP3">
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<Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
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<Residue name="TP3M">
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<Residue name="OH">
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<Bond atomName1="O1" atomName2="H1"/>
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<Residue name="LIT">
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<Residue name="SOD">
<Atom charge="1.0" name="SOD" type="SOD"/>
</Residue>
<Residue name="MG">
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</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"/>
<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"/>
</NonbondedForce>
<LennardJonesForce lj14scale="1.0">
<Atom epsilon="0.192464" sigma="0.04000135244450124" type="HT"/>
<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"/>
<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"/>
<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="0.2877602859593296" 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"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.2877602859593296" type1="OC2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28152399493234725" type1="OC2DP" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.2877602859593296" type1="OG2D2" type2="SOD"/>
<NBFixPair epsilon="0.31388368000000005" sigma="0.28152399493234725" type1="OG2P1" type2="SOD"/>
</LennardJonesForce>
</ForceField>
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 65920c60
...@@ -190,12 +190,16 @@ class ForceField(object): ...@@ -190,12 +190,16 @@ class ForceField(object):
method from which the forcefield XML data can be loaded. method from which the forcefield XML data can be loaded.
""" """
if not isinstance(files, tuple): if isinstance(files, tuple):
files = (files,) files = list(files)
else:
files = [files]
trees = [] trees = []
for file in files: i = 0
while i < len(files):
file = files[i]
tree = None tree = None
try: try:
# this handles either filenames or open file-like objects # this handles either filenames or open file-like objects
...@@ -221,12 +225,12 @@ class ForceField(object): ...@@ -221,12 +225,12 @@ class ForceField(object):
raise ValueError('Could not locate file "%s"' % file) raise ValueError('Could not locate file "%s"' % file)
trees.append(tree) trees.append(tree)
i += 1
# Process includes. # Process includes in this file.
for parentFile, tree in zip(files, trees): if isinstance(file, str):
if isinstance(parentFile, str): parentDir = os.path.dirname(file)
parentDir = os.path.dirname(parentFile)
else: else:
parentDir = '' parentDir = ''
for include in tree.getroot().findall('Include'): for include in tree.getroot().findall('Include'):
...@@ -234,7 +238,8 @@ class ForceField(object): ...@@ -234,7 +238,8 @@ class ForceField(object):
joined = os.path.join(parentDir, includeFile) joined = os.path.join(parentDir, includeFile)
if os.path.isfile(joined): if os.path.isfile(joined):
includeFile = joined includeFile = joined
self.loadFile(includeFile) if includeFile not in files:
files.append(includeFile)
# Load the atom types. # Load the atom types.
...@@ -2016,11 +2021,17 @@ class PeriodicTorsionGenerator(object): ...@@ -2016,11 +2021,17 @@ class PeriodicTorsionGenerator(object):
self.ff = forcefield self.ff = forcefield
self.proper = [] self.proper = []
self.improper = [] self.improper = []
self.propersForAtomType = defaultdict(set)
def registerProperTorsion(self, parameters): def registerProperTorsion(self, parameters):
torsion = self.ff._parseTorsion(parameters) torsion = self.ff._parseTorsion(parameters)
if torsion is not None: if torsion is not None:
index = len(self.proper)
self.proper.append(torsion) self.proper.append(torsion)
for t in torsion.types2:
self.propersForAtomType[t].add(index)
for t in torsion.types3:
self.propersForAtomType[t].add(index)
def registerImproperTorsion(self, parameters, ordering='default'): def registerImproperTorsion(self, parameters, ordering='default'):
torsion = self.ff._parseTorsion(parameters) torsion = self.ff._parseTorsion(parameters)
...@@ -2062,7 +2073,8 @@ class PeriodicTorsionGenerator(object): ...@@ -2062,7 +2073,8 @@ class PeriodicTorsionGenerator(object):
type3 = data.atomType[data.atoms[torsion[2]]] type3 = data.atomType[data.atoms[torsion[2]]]
type4 = data.atomType[data.atoms[torsion[3]]] type4 = data.atomType[data.atoms[torsion[3]]]
match = None match = None
for tordef in self.proper: for index in self.propersForAtomType[type2]:
tordef = self.proper[index]
types1 = tordef.types1 types1 = tordef.types1
types2 = tordef.types2 types2 = tordef.types2
types3 = tordef.types3 types3 = tordef.types3
...@@ -2391,7 +2403,7 @@ class LennardJonesGenerator(object): ...@@ -2391,7 +2403,7 @@ class LennardJonesGenerator(object):
paramsToMergedType[params] = len(mergedTypes) paramsToMergedType[params] = len(mergedTypes)
mergedTypes.append(t) mergedTypes.append(t)
mergedTypeParams.append(params) mergedTypeParams.append(params)
# Now everything is assigned. Create the A- and B-coefficient arrays # Now everything is assigned. Create the A- and B-coefficient arrays
numLjTypes = len(mergedTypes) numLjTypes = len(mergedTypes)
...@@ -2439,37 +2451,32 @@ class LennardJonesGenerator(object): ...@@ -2439,37 +2451,32 @@ class LennardJonesGenerator(object):
# Create the exceptions. # Create the exceptions.
bondIndices = _findBondsForExclusions(data, sys) bondIndices = _findBondsForExclusions(data, sys)
if self.lj14scale == 1: forceCopy = deepcopy(self.force)
# Just exclude the 1-2 and 1-3 interactions. forceCopy.createExclusionsFromBonds(bondIndices, 2)
self.force.createExclusionsFromBonds(bondIndices, 3)
self.force.createExclusionsFromBonds(bondIndices, 2) if self.force.getNumExclusions() > forceCopy.getNumExclusions() and self.lj14scale != 0:
else: # We need to create a CustomBondForce and use it to implement the scaled 1-4 interactions.
forceCopy = deepcopy(self.force)
forceCopy.createExclusionsFromBonds(bondIndices, 2) bonded = mm.CustomBondForce('%g*epsilon*((sigma/r)^12-(sigma/r)^6)' % (4*self.lj14scale))
self.force.createExclusionsFromBonds(bondIndices, 3) bonded.addPerBondParameter('sigma')
if self.force.getNumExclusions() > forceCopy.getNumExclusions() and self.lj14scale != 0: bonded.addPerBondParameter('epsilon')
# We need to create a CustomBondForce and use it to implement the scaled 1-4 interactions. sys.addForce(bonded)
skip = set(tuple(forceCopy.getExclusionParticles(i)) for i in range(forceCopy.getNumExclusions()))
bonded = mm.CustomBondForce('%g*epsilon*((sigma/r)^12-(sigma/r)^6)' % (4*self.lj14scale)) for i in range(self.force.getNumExclusions()):
bonded.addPerBondParameter('sigma') p1,p2 = self.force.getExclusionParticles(i)
bonded.addPerBondParameter('epsilon') a1 = data.atoms[p1]
sys.addForce(bonded) a2 = data.atoms[p2]
skip = set(tuple(forceCopy.getExclusionParticles(i)) for i in range(forceCopy.getNumExclusions())) if (p1,p2) not in skip and (p2,p1) not in skip:
for i in range(self.force.getNumExclusions()): type1 = data.atomType[a1]
p1,p2 = self.force.getExclusionParticles(i) type2 = data.atomType[a2]
a1 = data.atoms[p1] if (type1, type2) in self.nbfixTypes:
a2 = data.atoms[p2] sigma, epsilon = self.nbfixTypes[(type1, type2)]
if (p1,p2) not in skip and (p2,p1) not in skip: else:
type1 = data.atomType[a1] values1 = self.ljTypes.getAtomParameters(a1, data)
type2 = data.atomType[a2] values2 = self.ljTypes.getAtomParameters(a2, data)
if (type1, type2) in self.nbfixTypes: sigma = 0.5*(values1[0]+values2[0])
sigma, epsilon = self.nbfixTypes[(type1, type2)] epsilon = sqrt(values1[1]*values2[1])
else: bonded.addBond(p1, p2, (sigma, epsilon))
values1 = self.ljTypes.getAtomParameters(a1, data)
values2 = self.ljTypes.getAtomParameters(a2, data)
sigma = 0.5*(values1[0]+values2[0])
epsilon = sqrt(values1[1]*values2[1])
bonded.addBond(p1, p2, (sigma, epsilon))
parsers["LennardJonesForce"] = LennardJonesGenerator.parseElement parsers["LennardJonesForce"] = LennardJonesGenerator.parseElement
......
wrappers/python/simtk/openmm/app/topology.py
View file @ 65920c60
...@@ -155,6 +155,8 @@ class Topology(object): ...@@ -155,6 +155,8 @@ class Topology(object):
Residue Residue
the newly created Residue the newly created Residue
""" """
if len(chain._residues) > 0 and self._numResidues != chain._residues[-1].index+1:
raise ValueError('All residues within a chain must be contiguous')
if id is None: if id is None:
id = str(self._numResidues+1) id = str(self._numResidues+1)
residue = Residue(name, self._numResidues, chain, id) residue = Residue(name, self._numResidues, chain, id)
...@@ -182,6 +184,8 @@ class Topology(object): ...@@ -182,6 +184,8 @@ class Topology(object):
Atom Atom
the newly created Atom the newly created Atom
""" """
if len(residue._atoms) > 0 and self._numAtoms != residue._atoms[-1].index+1:
raise ValueError('All atoms within a residue must be contiguous')
if id is None: if id is None:
id = str(self._numAtoms+1) id = str(self._numAtoms+1)
atom = Atom(name, element, self._numAtoms, residue, id) atom = Atom(name, element, self._numAtoms, residue, id)
......
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