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4096 lines (4076 loc) · 221 KB
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<?xml version="1.0" encoding="UTF-8"?>
<ForceField>
<Info>
<DateGenerated>2022-03-18</DateGenerated>
<Reference>Robustelli, P., Piana, S., Shaw, D.E. (2018). Developing a molecular dynamics force field for both folded and disordered protein states. Proc Natl Acad Sci USA 115 (21), E4758-E4766.</Reference>
<Reference>Nguyen, H., Roe, D.R., Simmerling, C. (2013). Improved Generalized Born Solvent Model Parameters for Protein Simulations. J Chem Theor Comput 9 (4), 2020-2034.</Reference>
</Info>
<AtomTypes>
<Type element="C" name="C1" class="C1" mass="12.01"/>
<Type element="C" name="C8" class="C8" mass="12.01"/>
<Type element="C" name="C9" class="C9" mass="12.01"/>
<Type element="C" name="C10" class="C10" mass="12.01"/>
<Type element="O" name="O3" class="O3" mass="16.0"/>
<Type element="C" name="C" class="C" mass="12.01"/>
<Type element="C" name="CA" class="CA" mass="12.01"/>
<Type element="C" name="CB" class="CB" mass="12.01"/>
<Type element="C" name="CC" class="CC" mass="12.01"/>
<Type element="C" name="CD" class="CD" mass="12.01"/>
<Type element="C" name="CK" class="CK" mass="12.01"/>
<Type element="C" name="CM" class="CM" mass="12.01"/>
<Type element="C" name="CN" class="CN" mass="12.01"/>
<Type element="C" name="CQ" class="CQ" mass="12.01"/>
<Type element="C" name="CR" class="CR" mass="12.01"/>
<Type element="C" name="CT" class="CT" mass="12.01"/>
<Type element="C" name="CV" class="CV" mass="12.01"/>
<Type element="C" name="CW" class="CW" mass="12.01"/>
<Type element="C" name="C*" class="C*" mass="12.01"/>
<Type element="C" name="CY" class="CY" mass="12.01"/>
<Type element="C" name="CZ" class="CZ" mass="12.01"/>
<Type element="Ca" name="C0" class="C0" mass="40.08"/>
<Type element="H" name="H" class="H" mass="1.008"/>
<Type element="H" name="HB" class="HB" mass="1.008"/>
<Type element="H" name="HC" class="HC" mass="1.008"/>
<Type element="H" name="H1" class="H1" mass="1.008"/>
<Type element="H" name="H2" class="H2" mass="1.008"/>
<Type element="H" name="H3" class="H3" mass="1.008"/>
<Type element="H" name="HA" class="HA" mass="1.008"/>
<Type element="H" name="H4" class="H4" mass="1.008"/>
<Type element="H" name="H5" class="H5" mass="1.008"/>
<Type element="H" name="HO" class="HO" mass="1.008"/>
<Type element="H" name="HS" class="HS" mass="1.008"/>
<Type element="H" name="HW" class="HW" mass="1.008"/>
<Type element="H" name="HP" class="HP" mass="1.008"/>
<Type element="H" name="HZ" class="HZ" mass="1.008"/>
<Type element="F" name="F" class="F" mass="19.0"/>
<Type element="Cl" name="Cl" class="Cl" mass="35.45"/>
<Type element="Br" name="Br" class="Br" mass="79.9"/>
<Type element="I" name="I" class="I" mass="126.9"/>
<Type element="Cl" name="IM" class="IM" mass="35.45"/>
<Type element="Na" name="IB" class="IB" mass="131.0"/>
<Type element="Mg" name="MG" class="MG" mass="24.305"/>
<Type element="N" name="N" class="N" mass="14.01"/>
<Type element="N" name="NA" class="NA" mass="14.01"/>
<Type element="N" name="NB" class="NB" mass="14.01"/>
<Type element="N" name="NC" class="NC" mass="14.01"/>
<Type element="N" name="N2" class="N2" mass="14.01"/>
<Type element="N" name="N3" class="N3" mass="14.01"/>
<Type element="N" name="NT" class="NT" mass="14.01"/>
<Type element="N" name="N*" class="N*" mass="14.01"/>
<Type element="N" name="NY" class="NY" mass="14.01"/>
<Type element="O" name="O" class="O" mass="16.0"/>
<Type element="O" name="OB" class="OB" mass="16.0"/>
<Type element="O" name="O2" class="O2" mass="16.0"/>
<Type element="O" name="OW" class="OW" mass="16.0"/>
<Type element="O" name="OH" class="OH" mass="16.0"/>
<Type element="O" name="OS" class="OS" mass="16.0"/>
<Type element="P" name="P" class="P" mass="30.97"/>
<Type element="S" name="S" class="S" mass="32.06"/>
<Type element="S" name="SH" class="SH" mass="32.06"/>
<Type element="Cu" name="CU" class="CU" mass="63.55"/>
<Type element="Fe" name="FE" class="FE" mass="55.0"/>
<Type element="Li" name="Li" class="Li" mass="6.94"/>
<Type element="Na" name="IP" class="IP" mass="22.99"/>
<Type element="Na" name="Na" class="Na" mass="22.99"/>
<Type element="K" name="K" class="K" mass="39.1"/>
<Type element="Rb" name="Rb" class="Rb" mass="85.47"/>
<Type element="Cs" name="Cs" class="Cs" mass="132.91"/>
<Type element="Zn" name="Zn" class="Zn" mass="65.4"/>
<Type element="H" name="LP" class="LP" mass="3.0"/>
<Type element="C" name="C7" class="C7" mass="12.01"/>
<Type element="C" name="C3" class="C3" mass="12.01"/>
<Type element="C" name="C4" class="C4" mass="12.01"/>
<Type element="C" name="C5" class="C5" mass="12.01"/>
<Type element="C" name="C6" class="C6" mass="12.01"/>
</AtomTypes>
<Residues>
<Residue name="NALA">
<Atom name="N" type="N3" charge="0.1414"/>
<Atom name="H1" type="H" charge="0.1997"/>
<Atom name="H2" type="H" charge="0.1997"/>
<Atom name="H3" type="H" charge="0.1997"/>
<Atom name="CA" type="CT" charge="0.0962"/>
<Atom name="HA" type="HP" charge="0.0889"/>
<Atom name="CB" type="CT" charge="-0.0597"/>
<Atom name="HB1" type="HC" charge="0.03"/>
<Atom name="HB2" type="HC" charge="0.03"/>
<Atom name="HB3" type="HC" charge="0.03"/>
<Atom name="C" type="C" charge="0.6163"/>
<Atom name="O" type="O" charge="-0.5722"/>
<Bond atomName1="N" atomName2="H1"/>
<Bond atomName1="N" atomName2="H2"/>
<Bond atomName1="N" atomName2="H3"/>
<Bond atomName1="N" atomName2="CA"/>
<Bond atomName1="CA" atomName2="HA"/>
<Bond atomName1="CA" atomName2="CB"/>
<Bond atomName1="CB" atomName2="HB1"/>
<Bond atomName1="CB" atomName2="HB2"/>
<Bond atomName1="CB" atomName2="HB3"/>
<Bond atomName1="CA" atomName2="C"/>
<Bond atomName1="C" atomName2="O"/>
<ExternalBond atomName="C"/>
</Residue>
<Residue name="ASH">
<Atom name="N" type="N" charge="-0.4157"/>
<Atom name="H" type="H" charge="0.2719"/>
<Atom name="CA" type="CT" charge="0.0341"/>
<Atom name="HA" type="H1" charge="0.0864"/>
<Atom name="CB" type="CT" charge="-0.0316"/>
<Atom name="HB2" type="HC" charge="0.0488"/>
<Atom name="HB3" type="HC" charge="0.0488"/>
<Atom name="CG" type="C" charge="0.6462"/>
<Atom name="OD1" type="O" charge="-0.5554"/>
<Atom name="OD2" type="OH" charge="-0.6376"/>
<Atom name="HD2" type="HO" charge="0.4747"/>
<Atom name="C" type="C" charge="0.5973"/>
<Atom name="O" type="O" charge="-0.5679"/>
<Bond atomName1="N" atomName2="H"/>
<Bond atomName1="N" atomName2="CA"/>
<Bond atomName1="CA" atomName2="HA"/>
<Bond atomName1="CA" atomName2="CB"/>
<Bond atomName1="CB" atomName2="HB2"/>
<Bond atomName1="CB" atomName2="HB3"/>
<Bond atomName1="CB" atomName2="CG"/>
<Bond atomName1="CG" atomName2="OD1"/>
<Bond atomName1="CG" atomName2="OD2"/>
<Bond atomName1="OD2" atomName2="HD2"/>
<Bond atomName1="CA" atomName2="C"/>
<Bond atomName1="C" atomName2="O"/>
<ExternalBond atomName="N"/>
<ExternalBond atomName="C"/>
</Residue>
<Residue name="GLY">
<Atom name="N" type="N" charge="-0.4157"/>
<Atom name="H" type="H" charge="0.2719"/>
<Atom name="CA" type="C1" charge="-0.0252"/>
<Atom name="HA2" type="H1" charge="0.0698"/>
<Atom name="HA3" type="H1" charge="0.0698"/>
<Atom name="C" type="C" charge="0.5973"/>
<Atom name="O" type="O" charge="-0.5679"/>
<Bond atomName1="N" atomName2="H"/>
<Bond atomName1="N" atomName2="CA"/>
<Bond atomName1="CA" atomName2="HA2"/>
<Bond atomName1="CA" atomName2="HA3"/>
<Bond atomName1="CA" atomName2="C"/>
<Bond atomName1="C" atomName2="O"/>
<ExternalBond atomName="N"/>
<ExternalBond atomName="C"/>
</Residue>
<Residue name="NME">
<Atom name="N" type="N" charge="-0.4157"/>
<Atom name="H" type="H" charge="0.2719"/>
<Atom name="CH3" type="CT" charge="-0.149"/>
<Atom name="HH31" type="H1" charge="0.0976"/>
<Atom name="HH32" type="H1" charge="0.0976"/>
<Atom name="HH33" type="H1" charge="0.0976"/>
<Bond atomName1="N" atomName2="H"/>
<Bond atomName1="N" atomName2="CH3"/>
<Bond atomName1="CH3" atomName2="HH31"/>
<Bond atomName1="CH3" atomName2="HH32"/>
<Bond atomName1="CH3" atomName2="HH33"/>
<ExternalBond atomName="N"/>
</Residue>
<Residue name="ASN">
<Atom name="N" type="N" charge="-0.4157"/>
<Atom name="H" type="H" charge="0.2719"/>
<Atom name="CA" type="CT" charge="0.0143"/>
<Atom name="HA" type="H1" charge="0.1048"/>
<Atom name="CB" type="CT" charge="-0.2041"/>
<Atom name="HB2" type="HC" charge="0.0797"/>
<Atom name="HB3" type="HC" charge="0.0797"/>
<Atom name="CG" type="C5" charge="0.713"/>
<Atom name="OD1" type="O" charge="-0.5931"/>
<Atom name="ND2" type="N" charge="-0.9191"/>
<Atom name="HD21" type="H" charge="0.4196"/>
<Atom name="HD22" type="H" charge="0.4196"/>
<Atom name="C" type="C" charge="0.5973"/>
<Atom name="O" type="O" charge="-0.5679"/>
<Bond atomName1="N" atomName2="H"/>
<Bond atomName1="N" atomName2="CA"/>
<Bond atomName1="CA" atomName2="HA"/>
<Bond atomName1="CA" atomName2="CB"/>
<Bond atomName1="CB" atomName2="HB2"/>
<Bond atomName1="CB" atomName2="HB3"/>
<Bond atomName1="CB" atomName2="CG"/>
<Bond atomName1="CG" atomName2="OD1"/>
<Bond atomName1="CG" atomName2="ND2"/>
<Bond atomName1="ND2" atomName2="HD21"/>
<Bond atomName1="ND2" atomName2="HD22"/>
<Bond atomName1="CA" atomName2="C"/>
<Bond atomName1="C" atomName2="O"/>
<ExternalBond atomName="N"/>
<ExternalBond atomName="C"/>
</Residue>
<Residue name="CHIP">
<Atom name="N" type="N" charge="-0.3481"/>
<Atom name="H" type="H" charge="0.2764"/>
<Atom name="CA" type="CT" charge="-0.1445"/>
<Atom name="HA" type="H1" charge="0.1115"/>
<Atom name="CB" type="CT" charge="-0.08"/>
<Atom name="HB2" type="HC" charge="0.0868"/>
<Atom name="HB3" type="HC" charge="0.0868"/>
<Atom name="CG" type="CC" charge="0.0298"/>
<Atom name="ND1" type="NA" charge="-0.1501"/>
<Atom name="HD1" type="H" charge="0.3883"/>
<Atom name="CE1" type="CR" charge="-0.0251"/>
<Atom name="HE1" type="H5" charge="0.2694"/>
<Atom name="NE2" type="NA" charge="-0.1683"/>
<Atom name="HE2" type="H" charge="0.3913"/>
<Atom name="CD2" type="CW" charge="-0.1256"/>
<Atom name="HD2" type="H4" charge="0.2336"/>
<Atom name="C" type="C" charge="0.8032"/>
<Atom name="O" type="O2" charge="-0.8177"/>
<Atom name="OXT" type="O2" charge="-0.8177"/>
<Bond atomName1="N" atomName2="H"/>
<Bond atomName1="N" atomName2="CA"/>
<Bond atomName1="CA" atomName2="HA"/>
<Bond atomName1="CA" atomName2="CB"/>
<Bond atomName1="CB" atomName2="HB2"/>
<Bond atomName1="CB" atomName2="HB3"/>
<Bond atomName1="CB" atomName2="CG"/>
<Bond atomName1="CG" atomName2="ND1"/>
<Bond atomName1="ND1" atomName2="HD1"/>
<Bond atomName1="ND1" atomName2="CE1"/>
<Bond atomName1="CE1" atomName2="HE1"/>
<Bond atomName1="CE1" atomName2="NE2"/>
<Bond atomName1="NE2" atomName2="HE2"/>
<Bond atomName1="NE2" atomName2="CD2"/>
<Bond atomName1="CD2" atomName2="HD2"/>
<Bond atomName1="CA" atomName2="C"/>
<Bond atomName1="C" atomName2="O"/>
<Bond atomName1="C" atomName2="OXT"/>
<Bond atomName1="CG" atomName2="CD2"/>
<ExternalBond atomName="N"/>
</Residue>
<Residue name="CASP">
<Atom name="N" type="N" charge="-0.5192"/>
<Atom name="H" type="H" charge="0.3055"/>
<Atom name="CA" type="CT" charge="-0.1817"/>
<Atom name="HA" type="H1" charge="0.1046"/>
<Atom name="CB" type="CT" charge="-0.0677"/>
<Atom name="HB2" type="HC" charge="-0.0212"/>
<Atom name="HB3" type="HC" charge="-0.0212"/>
<Atom name="CG" type="C6" charge="0.8851"/>
<Atom name="OD1" type="O2" charge="-0.8162"/>
<Atom name="OD2" type="O2" charge="-0.8162"/>
<Atom name="C" type="C" charge="0.7256"/>
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