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Add OPC water model
cc: https://github.com/openmm/openmm/issues/2743
We just have to add leaprc.water.opc to the amber/biopolymers.yaml file.
@peastman : It looks like we actually have to add OPC parameters to OpenMM manually (as we did with other water models), and then we can build the versions that include the parameters for ions in openmmforcefields.
Check out the Amber20 manual.
Hi,
I'm making an attempt at adding the OPC water model, as we would like to use this at Cresset. I have manually generated an XML file for OPC water, using ParmEd and some trigonometry to work out the weights for the VirtualSite (see below). I think I next need to use this with the convert_amber.py script to add in the ions, but I haven't yet managed to make that script work. Using completely clean code, I have tried to regenerate the xml files for the existing solvent models using: 'python convert_amber.py --input solvents.yaml -v ', but this does not seem to work (I get a long and complicated xml file that does not match what was there before and an error from etree in the validation tests). Do you know if I am using the right command line arguments to convert_amber.py and if so does this work for you?
Understand this might not be top of your list right now, but if you are able to give any hints, that would be much appreciated!
Thanks,
Rosie
opc.xml:
<ForceField>
<AtomTypes>
<Type name="opc-O" class="opc-O" element="O" mass="15.99943"/>
<Type name="opc-H" class="opc-H" element="H" mass="1.007947"/>
<Type name="opc-M" class="opc-M" mass="0"/>
</AtomTypes>
<Residues>
<Residue name="HOH">
<Atom name="O" type="opc-O" charge="0"/>
<Atom name="H1" type="opc-H" charge="0.679142"/>
<Atom name="H2" type="opc-H" charge="0.679142"/>
<Atom name="M" type="opc-M" charge="-1.358284"/>
<VirtualSite type="average3" siteName="M" atomName1="O" atomName2="H1" atomName3="H2" weight1="0.7045553" weight2="0.1477224" weight3="0.1477224"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="opc-O" type2="opc-H" length="0.087243313" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="opc-H" type2="opc-O" type3="opc-H" angle="1.8081611051" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333333333" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom class="opc-O" epsilon="0.890359" sigma="0.316655"/>
<Atom class="opc-H" sigma="1" epsilon="0"/>
<Atom class="opc-M" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>
I see that no one has replied to this. @zhang-ivy and @jchodera do you have any idea? You're the ones most familiar with the convert_amber.py script.
Do you know if I am using the right command line arguments to convert_amber.py and if so does this work for you?
The command and arguments you are using look right to me (when I was converting the glycam forcefield, I was using python convert_amber.py -i glycam/glycan.yaml --verbose). The conversion pipeline in convert_amber.py may need updating depending on what's different in the new forcefields. I think we'll need @jchodera 's feedback here on what's necessary to convert the forcefield.
(I get a long and complicated xml file that does not match what was there before and an error from etree in the validation tests)
I'm not familiar with converting water model forcefields, but the xml you posted above doesn't look long and complicated to me.. could you elaborate on what's wrong with it?
Thanks so much for your reply. The xml file I posted is one created manually that contains details for just HOH. I think I need to use convert_amber.py to add the ion parameters to the xml. When I try to run the script for the existing water models (not adding any new ones), I get problems. With tip3p_standard.xml, I get the NonbondedForce section repeated for each new ion and I get multiple closing </ForceField> tags with one only one corresponding opening tag. I would be interested to know if rerunning convert_amber.py for the existing water models works for anybody else or if I am doing something wrong.
When I try to run the script for the existing water models (not adding any new ones), I get problems.
I'm also getting errors when I run python convert_amber.py --input solvents.yaml -v (using the same environment I used to convert the glycan forcefield):
Converting ['/home/zhangi/miniconda3/envs/glycan-ff-3/dat/leap/parm/frcmod.ionsjc_tip3p', '/home/zhangi/miniconda3/envs/glycan-ff-3/dat/leap/parm/frcmod.ions234lm_126_tip3p', '/home/zhangi/miniconda3/envs/glycan-ff-3/dat/leap/lib/atomic_ions.lib'] to ffxml...
odict_keys(['Li+', 'Na+', 'K+', 'Rb+', 'Cs+', 'F-', 'Cl-', 'Br-', 'I-', 'Be2+', 'Cu2+', 'Ni2+', 'Pt2+', 'Zn2+', 'Co2+', 'Pd2+', 'Ag2+', 'Cr2+', 'Fe2+', 'Mg2+', 'V2+', 'Mn2+', 'Hg2+', 'Cd2+', 'Yb2+', 'Ca2+', 'Sn2+', 'Pb2+', 'Eu2+', 'Sr2+', 'Sm2+', 'Ba2+', 'Ra2+', 'Al3+', 'Fe3+', 'Cr3+', 'In3+', 'Tl3+', 'Y3+', 'La3+', 'Ce3+', 'Pr3+', 'Nd3+', 'Sm3+', 'Eu3+', 'Gd3+', 'Tb3+', 'Dy3+', 'Er3+', 'Tm3+', 'Lu3+', 'Hf4+', 'Zr4+', 'Ce4+', 'U4+', 'Pu4+', 'Th4+'])
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:117: UserWarning: Residue AG contains atom type Ag+ not found in parameter set and will be dropped.
warnings.warn('Residue {} contains atom type {} not found in parameter set and will be dropped.'.format(residue.name, atom.type))
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:117: UserWarning: Residue CU1 contains atom type Cu+ not found in parameter set and will be dropped.
warnings.warn('Residue {} contains atom type {} not found in parameter set and will be dropped.'.format(residue.name, atom.type))
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:117: UserWarning: Residue H3O+ contains atom type H3O+ not found in parameter set and will be dropped.
warnings.warn('Residue {} contains atom type {} not found in parameter set and will be dropped.'.format(residue.name, atom.type))
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:117: UserWarning: Residue HE+ contains atom type HE+ not found in parameter set and will be dropped.
warnings.warn('Residue {} contains atom type {} not found in parameter set and will be dropped.'.format(residue.name, atom.type))
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:117: UserWarning: Residue HZ+ contains atom type HZ+ not found in parameter set and will be dropped.
warnings.warn('Residue {} contains atom type {} not found in parameter set and will be dropped.'.format(residue.name, atom.type))
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:117: UserWarning: Residue NH4 contains atom type NH4+ not found in parameter set and will be dropped.
warnings.warn('Residue {} contains atom type {} not found in parameter set and will be dropped.'.format(residue.name, atom.type))
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:117: UserWarning: Residue TL contains atom type Tl+ not found in parameter set and will be dropped.
warnings.warn('Residue {} contains atom type {} not found in parameter set and will be dropped.'.format(residue.name, atom.type))
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:351: ParameterWarning: Some residue templates using unavailable AtomTypes were found. They will not be written to the ffxml as write_unused is set to False
warnings.warn('Some residue templates using unavailable AtomTypes '
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:361: ParameterWarning: Some residue templates are using unavailable AtomTypes
warnings.warn('Some residue templates are using unavailable AtomTypes',
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:699: UserWarning: Skipping writing of residue <ResidueTemplate Cl-: 1 atoms; 0 bonds; head=None; tail=None> because OpenMM considers it identical to <ResidueTemplate CL: 1 atoms; 0 bonds; head=None; tail=None>
warnings.warn(f'Skipping writing of residue {residue} because OpenMM considers it identical to {residue_collision}')
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:699: UserWarning: Skipping writing of residue <ResidueTemplate K+: 1 atoms; 0 bonds; head=None; tail=None> because OpenMM considers it identical to <ResidueTemplate K: 1 atoms; 0 bonds; head=None; tail=None>
warnings.warn(f'Skipping writing of residue {residue} because OpenMM considers it identical to {residue_collision}')
/home/zhangi/miniconda3/envs/glycan-ff-3/lib/python3.8/site-packages/ParmEd-3.4.0+28.g3751049.dirty-py3.8-linux-x86_64.egg/parmed/openmm/parameters.py:699: UserWarning: Skipping writing of residue <ResidueTemplate Na+: 1 atoms; 0 bonds; head=None; tail=None> because OpenMM considers it identical to <ResidueTemplate NA: 1 atoms; 0 bonds; head=None; tail=None>
warnings.warn(f'Skipping writing of residue {residue} because OpenMM considers it identical to {residue_collision}')
Modifying converted ffxml to append solvent parameters
ffxml/tip3p_standard.xml successfully written!
Validating the conversion...
Water and ions energy validation for ffxml/tip3p_standard.xml
Preparing temporary files for validation...
Preparing LeaP scripts...
Running LEaP...
Traceback (most recent call last):
File "convert_amber.py", line 1577, in <module>
main()
File "convert_amber.py", line 112, in main
convert_yaml(args.input, ffxml_dir='ffxml/')
File "convert_amber.py", line 483, in convert_yaml
validate_water_ion(ffxml_name, files, solvent_name, recipe_name,
File "convert_amber.py", line 1125, in validate_water_ion
raise LeapException(leap_script_file[1])
__main__.LeapException: Something went wrong in processing this LEaP input file:
loadamberparams parm10.dat
loadamberparams /home/zhangi/miniconda3/envs/glycan-ff-3/dat/leap/parm/frcmod.ionsjc_tip3p
loadamberparams /home/zhangi/miniconda3/envs/glycan-ff-3/dat/leap/parm/frcmod.ions234lm_126_tip3p
loadOff atomic_ions.lib
loadoff solvents.lib
HOH = TP3
# for TIP4PEW
addPdbAtomMap {{ "M" "EPW" }}
x = loadPdb files/water_ion/tip3p_standard.pdb
saveAmberParm x /tmp/tmpcdq47yfg /tmp/tmpvxrwa73v
quit
And when I inspect tip3p_standard.xml, I'm seeing problems too:
tip3p_standard.xml.zip
I'm not sure why this is happening, you'll likely need to dive into the convert_amber.py script and see what's going on. It might be helpful to pull older versions of the script to see what changes cause the conversion pipeline to stop working.
I think the error you are seeing is because you are using a newer version of AmberTools. I fixed the above error by adding 'loadamberparams frcmod.tip3p' under 'loadamberparams parm10.dat', but unfortunately I still see problems (and also with older versions of AmberTools). I'll try having a look at the file history, thanks.
It's likely we're running into an issue with either (1) updates to ParmEd that break our conversion workflow, or (2) updates to the distributed versions of the LEaP input files that change what is being loaded.
It looks like our nightly CI runs are only testing the GAFF conversions, and not the solvent conversions. I'll open a PR to add the solvent conversions to the nightly tests to catch issues like this in the future, and dig a bit more into what is going on here.
It looks like AmberTools 21 broke everything. Working on this in #184 now.
I've made the full XML file for OPC with standard ions if you'd like to use it. I'm not associated with openmmforcefields and can't make any guarantees about this XML file but it's working in my tests.
Hope this is OK to post. Happy to do the work to integrate this properly into openmmforcefields once the problems with AmberTools21 are fixed.
<ForceField>
<Info>
<DateGenerated>2022-02-09</DateGenerated>
<Source Source="parm/frcmod.ionslm_126_opc" md5hash="61ee47ec99a7ebf66cf09e899a8f0581" sourcePackage="AmberTools" sourcePackageVersion="21.11">parm/frcmod.ionslm_126_opc</Source>
<Source Source="lib/atomic_ions.lib" md5hash="e900cee0c71ec2795d25b3555de486e1" sourcePackage="AmberTools" sourcePackageVersion="21.11">lib/atomic_ions.lib</Source>
<Source Source="parm/frcmod.opc" md5hash="cacffa2b26f52ac9ab9dedad93b2bd8f" sourcePackage="AmberTools" sourcePackageVersion="21.11">parm/frcmod.opc</Source>
<Source Source="lib/solvents.lib" md5hash="cb34b093bd93080e887d8849c4e8eea8" sourcePackage="AmberTools" sourcePackageVersion="21.11">lib/solvents.lib</Source>
<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>Izadi, S., Anandakrishnan R., and Onufriev, A.V. (2014). Building Water Models: A Different Approach. J. Phys. Chem. Lett. 5, 3863–3871.</Reference>
</Info>
<AtomTypes>
<Type element="Li" name="opc_standard-Li+" class="opc_standard-Li+" mass="6.94"/>
<Type element="Na" name="opc_standard-Na+" class="opc_standard-Na+" mass="22.99"/>
<Type element="K" name="opc_standard-K+" class="opc_standard-K+" mass="39.1"/>
<Type element="Rb" name="opc_standard-Rb+" class="opc_standard-Rb+" mass="85.47"/>
<Type element="Cs" name="opc_standard-Cs+" class="opc_standard-Cs+" mass="132.91"/>
<Type element="Tl" name="opc_standard-Tl+" class="opc_standard-Tl+" mass="204.38"/>
<Type element="Cu" name="opc_standard-Cu+" class="opc_standard-Cu+" mass="63.55"/>
<Type element="Ag" name="opc_standard-Ag+" class="opc_standard-Ag+" mass="107.87"/>
<Type element="F" name="opc_standard-F-" class="opc_standard-F-" mass="19.0"/>
<Type element="Cl" name="opc_standard-Cl-" class="opc_standard-Cl-" mass="35.45"/>
<Type element="Br" name="opc_standard-Br-" class="opc_standard-Br-" mass="79.9"/>
<Type element="I" name="opc_standard-I-" class="opc_standard-I-" mass="126.9"/>
<Type element="Be" name="opc_standard-Be2+" class="opc_standard-Be2+" mass="9.01"/>
<Type element="Cu" name="opc_standard-Cu2+" class="opc_standard-Cu2+" mass="63.55"/>
<Type element="Ni" name="opc_standard-Ni2+" class="opc_standard-Ni2+" mass="58.69"/>
<Type element="Pt" name="opc_standard-Pt2+" class="opc_standard-Pt2+" mass="195.08"/>
<Type element="Zn" name="opc_standard-Zn2+" class="opc_standard-Zn2+" mass="65.4"/>
<Type element="Co" name="opc_standard-Co2+" class="opc_standard-Co2+" mass="58.93"/>
<Type element="Pd" name="opc_standard-Pd2+" class="opc_standard-Pd2+" mass="106.42"/>
<Type element="Ag" name="opc_standard-Ag2+" class="opc_standard-Ag2+" mass="107.87"/>
<Type element="Cr" name="opc_standard-Cr2+" class="opc_standard-Cr2+" mass="52.0"/>
<Type element="Fe" name="opc_standard-Fe2+" class="opc_standard-Fe2+" mass="55.85"/>
<Type element="Mg" name="opc_standard-Mg2+" class="opc_standard-Mg2+" mass="24.305"/>
<Type element="V" name="opc_standard-V2+" class="opc_standard-V2+" mass="50.94"/>
<Type element="Mn" name="opc_standard-Mn2+" class="opc_standard-Mn2+" mass="54.94"/>
<Type element="Hg" name="opc_standard-Hg2+" class="opc_standard-Hg2+" mass="200.59"/>
<Type element="Cd" name="opc_standard-Cd2+" class="opc_standard-Cd2+" mass="112.41"/>
<Type element="Yb" name="opc_standard-Yb2+" class="opc_standard-Yb2+" mass="173.05"/>
<Type element="Ca" name="opc_standard-Ca2+" class="opc_standard-Ca2+" mass="40.08"/>
<Type element="Sn" name="opc_standard-Sn2+" class="opc_standard-Sn2+" mass="118.71"/>
<Type element="Pb" name="opc_standard-Pb2+" class="opc_standard-Pb2+" mass="207.2"/>
<Type element="Eu" name="opc_standard-Eu2+" class="opc_standard-Eu2+" mass="151.96"/>
<Type element="Sr" name="opc_standard-Sr2+" class="opc_standard-Sr2+" mass="87.62"/>
<Type element="Sm" name="opc_standard-Sm2+" class="opc_standard-Sm2+" mass="150.36"/>
<Type element="Ba" name="opc_standard-Ba2+" class="opc_standard-Ba2+" mass="137.33"/>
<Type element="Ra" name="opc_standard-Ra2+" class="opc_standard-Ra2+" mass="226.03"/>
<Type element="Al" name="opc_standard-Al3+" class="opc_standard-Al3+" mass="26.98"/>
<Type element="Fe" name="opc_standard-Fe3+" class="opc_standard-Fe3+" mass="55.85"/>
<Type element="Cr" name="opc_standard-Cr3+" class="opc_standard-Cr3+" mass="52.0"/>
<Type element="In" name="opc_standard-In3+" class="opc_standard-In3+" mass="114.82"/>
<Type element="Tl" name="opc_standard-Tl3+" class="opc_standard-Tl3+" mass="204.38"/>
<Type element="Y" name="opc_standard-Y3+" class="opc_standard-Y3+" mass="88.91"/>
<Type element="La" name="opc_standard-La3+" class="opc_standard-La3+" mass="138.91"/>
<Type element="Ce" name="opc_standard-Ce3+" class="opc_standard-Ce3+" mass="140.12"/>
<Type element="Pr" name="opc_standard-Pr3+" class="opc_standard-Pr3+" mass="140.91"/>
<Type element="Nd" name="opc_standard-Nd3+" class="opc_standard-Nd3+" mass="144.24"/>
<Type element="Sm" name="opc_standard-Sm3+" class="opc_standard-Sm3+" mass="150.36"/>
<Type element="Eu" name="opc_standard-Eu3+" class="opc_standard-Eu3+" mass="151.96"/>
<Type element="Gd" name="opc_standard-Gd3+" class="opc_standard-Gd3+" mass="157.25"/>
<Type element="Tb" name="opc_standard-Tb3+" class="opc_standard-Tb3+" mass="158.93"/>
<Type element="Dy" name="opc_standard-Dy3+" class="opc_standard-Dy3+" mass="162.5"/>
<Type element="Er" name="opc_standard-Er3+" class="opc_standard-Er3+" mass="167.26"/>
<Type element="Tm" name="opc_standard-Tm3+" class="opc_standard-Tm3+" mass="168.93"/>
<Type element="Lu" name="opc_standard-Lu3+" class="opc_standard-Lu3+" mass="174.97"/>
<Type element="Hf" name="opc_standard-Hf4+" class="opc_standard-Hf4+" mass="178.49"/>
<Type element="Zr" name="opc_standard-Zr4+" class="opc_standard-Zr4+" mass="91.22"/>
<Type element="Ce" name="opc_standard-Ce4+" class="opc_standard-Ce4+" mass="140.12"/>
<Type element="U" name="opc_standard-U4+" class="opc_standard-U4+" mass="238.03"/>
<Type element="Pu" name="opc_standard-Pu4+" class="opc_standard-Pu4+" mass="244.06"/>
<Type element="Th" name="opc_standard-Th4+" class="opc_standard-Th4+" mass="232.04"/>
<Type name="opc-O" class="opc-O" element="O" mass="15.99943"/>
<Type name="opc-H" class="opc-H" element="H" mass="1.007947"/>
<Type name="opc-M" class="opc-M" mass="0"/>
</AtomTypes>
<Residues>
<Residue name="AG">
<Atom name="AG" type="opc_standard-Ag+" charge="1.0"/>
</Residue>
<Residue name="AL">
<Atom name="AL" type="opc_standard-Al3+" charge="3.0"/>
</Residue>
<Residue name="Ag">
<Atom name="Ag" type="opc_standard-Ag2+" charge="2.0"/>
</Residue>
<Residue name="BA">
<Atom name="BA" type="opc_standard-Ba2+" charge="2.0"/>
</Residue>
<Residue name="BR">
<Atom name="BR" type="opc_standard-Br-" charge="-1.0"/>
</Residue>
<Residue name="Be">
<Atom name="Be" type="opc_standard-Be2+" charge="2.0"/>
</Residue>
<Residue name="CA">
<Atom name="CA" type="opc_standard-Ca2+" charge="2.0"/>
</Residue>
<Residue name="CD">
<Atom name="CD" type="opc_standard-Cd2+" charge="2.0"/>
</Residue>
<Residue name="CE">
<Atom name="CE" type="opc_standard-Ce3+" charge="3.0"/>
</Residue>
<Residue name="CL">
<Atom name="CL" type="opc_standard-Cl-" charge="-1.0"/>
</Residue>
<Residue name="CO">
<Atom name="CO" type="opc_standard-Co2+" charge="2.0"/>
</Residue>
<Residue name="CR">
<Atom name="CR" type="opc_standard-Cr3+" charge="3.0"/>
</Residue>
<Residue name="CS">
<Atom name="CS" type="opc_standard-Cs+" charge="1.0"/>
</Residue>
<Residue name="CU">
<Atom name="CU" type="opc_standard-Cu2+" charge="2.0"/>
</Residue>
<Residue name="CU1">
<Atom name="CU" type="opc_standard-Cu+" charge="1.0"/>
</Residue>
<Residue name="Ce">
<Atom name="Ce" type="opc_standard-Ce4+" charge="4.0"/>
</Residue>
<Residue name="Cr">
<Atom name="Cr" type="opc_standard-Cr2+" charge="2.0"/>
</Residue>
<Residue name="Dy">
<Atom name="Dy" type="opc_standard-Dy3+" charge="3.0"/>
</Residue>
<Residue name="EU">
<Atom name="EU" type="opc_standard-Eu2+" charge="2.0"/>
</Residue>
<Residue name="EU3">
<Atom name="EU3" type="opc_standard-Eu3+" charge="3.0"/>
</Residue>
<Residue name="Er">
<Atom name="Er" type="opc_standard-Er3+" charge="3.0"/>
</Residue>
<Residue name="F">
<Atom name="F" type="opc_standard-F-" charge="-1.0"/>
</Residue>
<Residue name="FE">
<Atom name="FE" type="opc_standard-Fe3+" charge="3.0"/>
</Residue>
<Residue name="FE2">
<Atom name="FE2" type="opc_standard-Fe2+" charge="2.0"/>
</Residue>
<Residue name="GD3">
<Atom name="GD" type="opc_standard-Gd3+" charge="3.0"/>
</Residue>
<Residue name="HG">
<Atom name="HG" type="opc_standard-Hg2+" charge="2.0"/>
</Residue>
<Residue name="Hf">
<Atom name="Hf" type="opc_standard-Hf4+" charge="4.0"/>
</Residue>
<Residue name="IN">
<Atom name="IN" type="opc_standard-In3+" charge="3.0"/>
</Residue>
<Residue name="IOD">
<Atom name="I" type="opc_standard-I-" charge="-1.0"/>
</Residue>
<Residue name="K">
<Atom name="K" type="opc_standard-K+" charge="1.0"/>
</Residue>
<Residue name="LA">
<Atom name="LA" type="opc_standard-La3+" charge="3.0"/>
</Residue>
<Residue name="LI">
<Atom name="LI" type="opc_standard-Li+" charge="1.0"/>
</Residue>
<Residue name="LU">
<Atom name="LU" type="opc_standard-Lu3+" charge="3.0"/>
</Residue>
<Residue name="MG">
<Atom name="MG" type="opc_standard-Mg2+" charge="2.0"/>
</Residue>
<Residue name="MN">
<Atom name="MN" type="opc_standard-Mn2+" charge="2.0"/>
</Residue>
<Residue name="NA">
<Atom name="NA" type="opc_standard-Na+" charge="1.0"/>
</Residue>
<Residue name="NI">
<Atom name="NI" type="opc_standard-Ni2+" charge="2.0"/>
</Residue>
<Residue name="Nd">
<Atom name="Nd" type="opc_standard-Nd3+" charge="3.0"/>
</Residue>
<Residue name="PB">
<Atom name="PB" type="opc_standard-Pb2+" charge="2.0"/>
</Residue>
<Residue name="PD">
<Atom name="PD" type="opc_standard-Pd2+" charge="2.0"/>
</Residue>
<Residue name="PR">
<Atom name="PR" type="opc_standard-Pr3+" charge="3.0"/>
</Residue>
<Residue name="PT">
<Atom name="PT" type="opc_standard-Pt2+" charge="2.0"/>
</Residue>
<Residue name="Pu">
<Atom name="Pu" type="opc_standard-Pu4+" charge="4.0"/>
</Residue>
<Residue name="RB">
<Atom name="RB" type="opc_standard-Rb+" charge="1.0"/>
</Residue>
<Residue name="Ra">
<Atom name="Ra" type="opc_standard-Ra2+" charge="2.0"/>
</Residue>
<Residue name="SM">
<Atom name="SM" type="opc_standard-Sm3+" charge="3.0"/>
</Residue>
<Residue name="SR">
<Atom name="SR" type="opc_standard-Sr2+" charge="2.0"/>
</Residue>
<Residue name="Sm">
<Atom name="Sm" type="opc_standard-Sm2+" charge="2.0"/>
</Residue>
<Residue name="Sn">
<Atom name="Sn" type="opc_standard-Sn2+" charge="2.0"/>
</Residue>
<Residue name="TB">
<Atom name="TB" type="opc_standard-Tb3+" charge="3.0"/>
</Residue>
<Residue name="TL">
<Atom name="TL" type="opc_standard-Tl+" charge="1.0"/>
</Residue>
<Residue name="Th">
<Atom name="Th" type="opc_standard-Th4+" charge="4.0"/>
</Residue>
<Residue name="Tl">
<Atom name="Tl" type="opc_standard-Tl3+" charge="3.0"/>
</Residue>
<Residue name="Tm">
<Atom name="Tm" type="opc_standard-Tm3+" charge="3.0"/>
</Residue>
<Residue name="U4+">
<Atom name="U" type="opc_standard-U4+" charge="4.0"/>
</Residue>
<Residue name="V2+">
<Atom name="V2+" type="opc_standard-V2+" charge="2.0"/>
</Residue>
<Residue name="Y">
<Atom name="Y" type="opc_standard-Y3+" charge="3.0"/>
</Residue>
<Residue name="YB2">
<Atom name="YB2" type="opc_standard-Yb2+" charge="2.0"/>
</Residue>
<Residue name="ZN">
<Atom name="ZN" type="opc_standard-Zn2+" charge="2.0"/>
</Residue>
<Residue name="Zr">
<Atom name="Zr" type="opc_standard-Zr4+" charge="4.0"/>
</Residue>
<Residue name="HOH">
<Atom name="O" type="opc-O" charge="0"/>
<Atom name="H1" type="opc-H" charge="0.679142"/>
<Atom name="H2" type="opc-H" charge="0.679142"/>
<Atom name="M" type="opc-M" charge="-1.358284"/>
<VirtualSite type="average3" siteName="M" atomName1="O" atomName2="H1" atomName3="H2" weight1="0.70455878106" weight2="0.14772060947" weight3="0.14772060947"/>
<Bond atomName1="O" atomName2="H1"/>
<Bond atomName1="O" atomName2="H2"/>
</Residue>
</Residues>
<HarmonicBondForce>
<Bond type1="opc-O" type2="opc-H" length="0.087243313" k="462750.4"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="opc-H" type2="opc-O" type3="opc-H" angle="1.80816110507" k="836.8"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
<UseAttributeFromResidue name="charge"/>
<Atom type="opc_standard-Li+" sigma="0.2212992415860603" epsilon="0.009039866720000001"/>
<Atom type="opc_standard-Na+" sigma="0.26138968390237555" epsilon="0.12386075112"/>
<Atom type="opc_standard-K+" sigma="0.3032619236549715" epsilon="0.58382766144"/>
<Atom type="opc_standard-Rb+" sigma="0.3239307739158274" epsilon="0.9537620464000001"/>
<Atom type="opc_standard-Cs+" sigma="0.349232297511013" epsilon="1.47731805816"/>
<Atom type="opc_standard-Tl+" sigma="0.29577837442259264" epsilon="0.47070573208000005"/>
<Atom type="opc_standard-Cu+" sigma="0.21025209748112006" epsilon="0.0032724319200000004"/>
<Atom type="opc_standard-Ag+" sigma="0.23448454261453733" epsilon="0.025210566480000002"/>
<Atom type="opc_standard-F-" sigma="0.3278507282756449" epsilon="1.0313754556"/>
<Atom type="opc_standard-Cl-" sigma="0.4205041949622401" epsilon="2.8400519208"/>
<Atom type="opc_standard-Br-" sigma="0.4452711793265416" epsilon="3.17863094952"/>
<Atom type="opc_standard-I-" sigma="0.5167212565213968" epsilon="3.77817463544"/>
<Atom type="opc_standard-Be2+" sigma="0.16410354388145051" epsilon="5.35552e-06"/>
<Atom type="opc_standard-Cu2+" sigma="0.20989573799386393" epsilon="0.0031585016"/>
<Atom type="opc_standard-Ni2+" sigma="0.21328115312279727" epsilon="0.00439211216"/>
<Atom type="opc_standard-Pt2+" sigma="0.21720110748261476" epsilon="0.00631378152"/>
<Atom type="opc_standard-Zn2+" sigma="0.21720110748261476" epsilon="0.00631378152"/>
<Atom type="opc_standard-Co2+" sigma="0.2250410162022497" epsilon="0.012329536720000001"/>
<Atom type="opc_standard-Pd2+" sigma="0.2261100946640181" epsilon="0.013433485120000001"/>
<Atom type="opc_standard-Ag2+" sigma="0.23252456543462854" epsilon="0.0218984284"/>
<Atom type="opc_standard-Cr2+" sigma="0.23448454261453733" epsilon="0.025210566480000002"/>
<Atom type="opc_standard-Fe2+" sigma="0.23573180081993375" epsilon="0.027520218160000002"/>
<Atom type="opc_standard-Mg2+" sigma="0.23697905902533029" epsilon="0.0299963512"/>
<Atom type="opc_standard-V2+" sigma="0.23769177799984254" epsilon="0.03148911872"/>
<Atom type="opc_standard-Mn2+" sigma="0.2460662259503617" epsilon="0.053825486400000004"/>
<Atom type="opc_standard-Hg2+" sigma="0.2460662259503617" epsilon="0.053825486400000004"/>
<Atom type="opc_standard-Cd2+" sigma="0.24749166389938626" epsilon="0.05861307024"/>
<Atom type="opc_standard-Yb2+" sigma="0.2854439492921647" epsilon="0.33615222504000003"/>
<Atom type="opc_standard-Ca2+" sigma="0.2865130277539331" epsilon="0.34886028824000004"/>
<Atom type="opc_standard-Sn2+" sigma="0.2895420833956103" epsilon="0.38639884336"/>
<Atom type="opc_standard-Pb2+" sigma="0.30415282237311186" epsilon="0.59811815528"/>
<Atom type="opc_standard-Eu2+" sigma="0.31234909058000293" epsilon="0.73715046696"/>
<Atom type="opc_standard-Sr2+" sigma="0.31466542724716784" epsilon="0.77874118424"/>
<Atom type="opc_standard-Sm2+" sigma="0.31466542724716784" epsilon="0.77874118424"/>
<Atom type="opc_standard-Ba2+" sigma="0.349232297511013" epsilon="1.47731805816"/>
<Atom type="opc_standard-Ra2+" sigma="0.349232297511013" epsilon="1.47731805816"/>
<Atom type="opc_standard-Al3+" sigma="0.22272467953508485" epsilon="0.010193772080000002"/>
<Atom type="opc_standard-Fe3+" sigma="0.249451641079295" epsilon="0.06572013816000001"/>
<Atom type="opc_standard-Cr3+" sigma="0.2380481374870987" epsilon="0.032257342960000004"/>
<Atom type="opc_standard-In3+" sigma="0.2565788308244177" epsilon="0.09715545064"/>
<Atom type="opc_standard-Tl3+" sigma="0.26424055980042466" epsilon="0.14196839183999999"/>
<Atom type="opc_standard-Y3+" sigma="0.2806330962142069" epsilon="0.28247819944"/>
<Atom type="opc_standard-La3+" sigma="0.30290556416771536" epsilon="0.5781589690400001"/>
<Atom type="opc_standard-Ce3+" sigma="0.30736005775841707" epsilon="0.65093680392"/>
<Atom type="opc_standard-Pr3+" sigma="0.30593461980939257" epsilon="0.62720034432"/>
<Atom type="opc_standard-Nd3+" sigma="0.29613473390984874" epsilon="0.47580293192"/>
<Atom type="opc_standard-Sm3+" sigma="0.2918584200627751" epsilon="0.41662062848000003"/>
<Atom type="opc_standard-Eu3+" sigma="0.2932838580117997" epsilon="0.43586389048"/>
<Atom type="opc_standard-Gd3+" sigma="0.2850875898049086" epsilon="0.33197918711999996"/>
<Atom type="opc_standard-Tb3+" sigma="0.2865130277539331" epsilon="0.34886028824000004"/>
<Atom type="opc_standard-Dy3+" sigma="0.2820585341632314" epsilon="0.29778189072"/>
<Atom type="opc_standard-Er3+" sigma="0.2806330962142069" epsilon="0.28247819944"/>
<Atom type="opc_standard-Tm3+" sigma="0.2806330962142069" epsilon="0.28247819944"/>
<Atom type="opc_standard-Lu3+" sigma="0.27760404057252974" epsilon="0.25163082264000003"/>
<Atom type="opc_standard-Hf4+" sigma="0.26032060544060714" epsilon="0.11751709584"/>
<Atom type="opc_standard-Zr4+" sigma="0.26513145851856496" epsilon="0.14799067408"/>
<Atom type="opc_standard-Ce4+" sigma="0.2998765085260382" epsilon="0.5310938643199999"/>
<Atom type="opc_standard-U4+" sigma="0.2998765085260382" epsilon="0.5310938643199999"/>
<Atom type="opc_standard-Pu4+" sigma="0.29542201493533654" epsilon="0.46563832232"/>
<Atom type="opc_standard-Th4+" sigma="0.3036182831422276" epsilon="0.58952354984"/>
<Atom type="opc-O" sigma="0.3166552081964338" epsilon="0.8903586015920001"/>
<Atom type="opc-H" sigma="1" epsilon="0"/>
<Atom type="opc-M" sigma="1" epsilon="0"/>
</NonbondedForce>
</ForceField>`