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Improper debugging
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<ForceField> | |
<AtomTypes> | |
<Type name="c" class="c" element="C" mass="12.01" def="[C;X3][O&X1,S&X1]" desc="Sp2 C carbonyl group" doi="10.1002/jcc/20035"/> | |
<Type name="h5" class="h5" element="H" mass="1.008" def="H[C;!X4]([N,O,F,Cl,Br,I,S])([N,O,F,Cl,Br,I,S])" desc="H bonded to non-sp3 carbon with 2 d. group" doi="10.1002/jcc/20035"/> | |
<Type name="ho" class="ho" element="H" mass="1.008" def="HO" desc="Hydroxyl group" doi="10.1002/jcc/20035"/> | |
<Type name="o" class="o" element="O" mass="16.00" def="[O;X1]" desc="Oxygen with one connected atom" doi="10.1002/jcc/20035"/> | |
<Type name="oh" class="oh" element="O" mass="16.00" def="[O;X2]H" desc="Oxygen in hydroxyl group" doi="10.1002/jcc/20035"/> | |
</AtomTypes> | |
<NonbondedForce coulomb14scale="0.833333333" lj14scale="0.5"> | |
<Atom type="c" charge="0.0" sigma="0.33996695084235345" epsilon="0.359824"/> | |
<Atom type="h5" charge="0.0" sigma="0.2421462715905442" epsilon="0.06276"/> | |
<Atom type="ho" charge="0.0" sigma="0.0" epsilon="0.0"/> | |
<Atom type="o" charge="0.0" sigma="0.2959921901149464" epsilon="0.87864"/> | |
<Atom type="oh" charge="0.0" sigma="0.3066473387839048" epsilon="0.8803136"/> | |
</NonbondedForce> | |
<HarmonicBondForce> | |
<Bond class1="c" class2="o" length="0.12183" k="533627.36"/> | |
<Bond class1="c" class2="oh" length="0.13513" k="334803.68"/> | |
<Bond class1="c" class2="h5" length="0.11051" k="267524.95999999996"/> | |
<Bond class1="ho" class2="oh" length="0.0973" k="310787.51999999996"/> | |
</HarmonicBondForce> | |
<HarmonicAngleForce> | |
<Angle class1="c" class2="oh" class3="ho" angle="1.8596483179999581" k="417.5632"/> | |
<Angle class1="o" class2="c" class3="oh" angle="2.131047016685076" k="635.1312"/> | |
<Angle class1="h5" class2="c" class3="o" angle="2.1580996200909888" k="449.36160000000007"/> | |
<Angle class1="h5" class2="c" class3="oh" angle="1.9109609980085913" k="444.3408"/> | |
</HarmonicAngleForce> | |
<PeriodicTorsionForce> | |
<Proper class1="" class2="c" class3="oh" class4="" periodicity1="2" k1="9.623199999999999" phase1="3.141592653589793"/> | |
<Improper class1="c" class2="" class3="oh" class4="o" periodicity1="2" k1="4.6024" phase1="3.141592653589793"/> | |
</PeriodicTorsionForce> | |
</ForceField> |
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import foyer | |
import mbuild | |
mol = mbuild.load("C(=O)O", smiles=True) | |
ff = foyer.Forcefield("improper_amber.xml") | |
mol_ff = ff.apply(mol) | |
mol_ff.save("test.gro", overwrite=True) | |
mol_ff.save("test.top", overwrite=True) | |
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