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Commit 7f067d28 authored by peastman's avatar peastman
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Fixes to CHARMM36 force field

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wrappers/python/simtk/openmm/app/data/charmm36.xml
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wrappers/python/simtk/openmm/app/data/charmm36/spce.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_spc.str" md5hash="0d8c56cbaa3d3fa6fd0352e11826c12d" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_spc.str</Source> <Source Source="toppar/non_charmm/toppar_water_ions_spc_e.str" md5hash="7a0187836503ba10b8f8207f06f51075" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_spc_e.str</Source>
<Reference Reference="H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans. INTERACTION MODELS FOR WATER IN RELATION TO PROTEIN HYDRATION In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), p. 331" forcefield="spc">H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans. INTERACTION MODELS FOR WATER IN RELATION TO PROTEIN HYDRATION In Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), p. 331</Reference> <Reference Reference="H.J.C. Berendsen, J. R. Grigera, and T. P. Straatsma. The Missing Term in Effective Pair Potentials. J. Phys. Chem 91:6269-6271, 1987." forcefield="spc-e">H.J.C. Berendsen, J. R. Grigera, and T. P. Straatsma. The Missing Term in Effective Pair Potentials. J. Phys. Chem 91:6269-6271, 1987.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference> <Reference Reference="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="['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> </Info>
...@@ -24,13 +24,12 @@ ...@@ -24,13 +24,12 @@
<Type class="CLA" element="Cl" mass="35.45" name="CLA"/> <Type class="CLA" element="Cl" mass="35.45" name="CLA"/>
</AtomTypes> </AtomTypes>
<Residues> <Residues>
<Residue name="SPC"> <Residue name="SPCE">
<Atom charge="-0.8068" name="OH2" type="OT"/> <Atom charge="-0.8476" name="OH2" type="OT"/>
<Atom charge="0.4034" name="H1" type="HT"/> <Atom charge="0.4238" name="H1" type="HT"/>
<Atom charge="0.4034" name="H2" type="HT"/> <Atom charge="0.4238" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
</Residue> </Residue>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/data/charmm36/tip3p-pme-b.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str" md5hash="52fc5f1cff9a0a88ea24adf588612a54" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str</Source> <Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str" md5hash="52fc5f1cff9a0a88ea24adf588612a54" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_b.str</Source>
<Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-b">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference> <Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-b">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference> <Reference Reference="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>
...@@ -30,7 +30,6 @@ ...@@ -30,7 +30,6 @@
<Atom charge="0.415" name="H2" type="HT"/> <Atom charge="0.415" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
</Residue> </Residue>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/data/charmm36/tip3p-pme-f.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</DateGenerated>
<Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str" md5hash="0f345cc879086d43d9fb62392a426fd3" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str</Source> <Source Source="toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str" md5hash="0f345cc879086d43d9fb62392a426fd3" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/non_charmm/toppar_water_ions_tip3p_pme_f.str</Source>
<Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-f">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference> <Reference Reference="D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004." forcefield="tip3p-pme-f">D.J. Price and C.L. Brooks III. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 121:10096-10103, 2004.</Reference>
<Reference Reference="Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063" forcefield="ions">Beglov, D. and Roux, B., Finite Representation of an Infinite Bulk System: Solvent Boundary Potential for Computer Simulations, Journal of Chemical Physics, 1994, 100: 9050-9063</Reference> <Reference Reference="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>
...@@ -30,7 +30,6 @@ ...@@ -30,7 +30,6 @@
<Atom charge="0.415" name="H2" type="HT"/> <Atom charge="0.415" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/>
</Residue> </Residue>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/data/charmm36/tip4p2005.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</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> <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="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="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>
...@@ -32,8 +32,7 @@ ...@@ -32,8 +32,7 @@
<Atom charge="0.5564" name="H2" type="HT"/> <Atom charge="0.5564" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/> <VirtualSite atomName1="OH2" atomName2="H1" atomName3="H2" index="0" p1="0.015459999999999998" p2="0" p3="0" siteName="OM" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1"/>
<Bond atomName1="OH2" atomName2="OM"/>
</Residue> </Residue>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/data/charmm36/tip4pew.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</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> <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="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="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>
...@@ -32,8 +32,7 @@ ...@@ -32,8 +32,7 @@
<Atom charge="0.52422" name="H2" type="HT"/> <Atom charge="0.52422" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/> <VirtualSite atomName1="OH2" atomName2="H1" atomName3="H2" index="0" p1="0.0125" p2="0" p3="0" siteName="OM" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1"/>
<Bond atomName1="OH2" atomName2="OM"/>
</Residue> </Residue>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/data/charmm36/tip5p.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</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> <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="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="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>
...@@ -33,9 +33,8 @@ ...@@ -33,9 +33,8 @@
<Atom charge="-0.241" name="LP2" type="LP"/> <Atom charge="-0.241" name="LP2" type="LP"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/> <VirtualSite atomName1="OH2" atomName2="H1" atomName3="H2" index="0" p1="-0.04041512765608711" p2="0" p3="0.057154330164408206" siteName="LP1" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1"/>
<Bond atomName1="OH2" atomName2="LP1"/> <VirtualSite atomName1="OH2" atomName2="H1" atomName3="H2" index="1" p1="-0.04041512765608711" p2="0" p3="-0.057154330164408206" siteName="LP2" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1"/>
<Bond atomName1="OH2" atomName2="LP2"/>
</Residue> </Residue>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/data/charmm36/tip5pew.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</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> <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="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="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>
...@@ -33,9 +33,8 @@ ...@@ -33,9 +33,8 @@
<Atom charge="-0.241" name="LP2" type="LP"/> <Atom charge="-0.241" name="LP2" type="LP"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <Bond atomName1="OH2" atomName2="H2"/>
<Bond atomName1="H1" atomName2="H2"/> <VirtualSite atomName1="OH2" atomName2="H1" atomName3="H2" index="0" p1="-0.04041512765608711" p2="0" p3="0.057154330164408206" siteName="LP1" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1"/>
<Bond atomName1="OH2" atomName2="LP1"/> <VirtualSite atomName1="OH2" atomName2="H1" atomName3="H2" index="1" p1="-0.04041512765608711" p2="0" p3="-0.057154330164408206" siteName="LP2" type="localCoords" wo1="1" wo2="0" wo3="0" wx1="-1.0" wx2="0.5" wx3="0.5" wy1="0" wy2="-1" wy3="1"/>
<Bond atomName1="OH2" atomName2="LP2"/>
</Residue> </Residue>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/data/charmm36/water.xml
View file @ 7f067d28
<ForceField> <ForceField>
<Info> <Info>
<DateGenerated>2017-11-26</DateGenerated> <DateGenerated>2018-01-26</DateGenerated>
<Source Source="toppar/toppar_water_ions.str" md5hash="f59e96950d55df9ca4f9b2d1486d7f4f" sourcePackage="charmm36" sourcePackageVersion="toppar_c36_aug15.tgz">toppar/toppar_water_ions.str</Source> <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="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="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>
...@@ -31,14 +31,6 @@ ...@@ -31,14 +31,6 @@
<Atom charge="0.417" name="H2" type="HT"/> <Atom charge="0.417" name="H2" type="HT"/>
<Bond atomName1="OH2" atomName2="H1"/> <Bond atomName1="OH2" atomName2="H1"/>
<Bond atomName1="OH2" atomName2="H2"/> <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>
<Residue name="OH"> <Residue name="OH">
<Atom charge="-1.32" name="O1" type="OX"/> <Atom charge="-1.32" name="O1" type="OX"/>
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 7f067d28
...@@ -1404,8 +1404,9 @@ def _matchResidue(res, template, bondedToAtom, ignoreExternalBonds=False): ...@@ -1404,8 +1404,9 @@ def _matchResidue(res, template, bondedToAtom, ignoreExternalBonds=False):
candidates = [[] for i in range(numAtoms)] candidates = [[] for i in range(numAtoms)]
for i in range(numAtoms): for i in range(numAtoms):
exactNameMatch = (atoms[i].element is None and any(atom.element is None and atom.name == atoms[i].name for atom in template.atoms))
for j, atom in enumerate(template.atoms): for j, atom in enumerate(template.atoms):
if (atom.element is not None and atom.element != atoms[i].element) or (atom.element is None and atom.name != atoms[i].name): if (atom.element is not None and atom.element != atoms[i].element) or (exactNameMatch and atom.name != atoms[i].name):
continue continue
if len(atom.bondedTo) != len(bondedTo[i]): if len(atom.bondedTo) != len(bondedTo[i]):
continue continue
......
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