Skip to content

GitLab

Unverified Commit edee11b6 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
Browse files

Fix errors with AMOEBA 2018 (#3311)

parent 27bcb657
Hide whitespace changes
Inline Side-by-side
Showing with 125 additions and 125 deletions
devtools/forcefield-scripts/processTinkerForceField.py
View file @ edee11b6
......@@ -679,8 +679,10 @@ tinkerXmlFile.write( " </AtomTypes>\n")
tinkerXmlFile.write( " <Residues>\n" )
for resname, res in sorted(residueDict.items()):
if res['include']:
outputString = """ <Residue name="%s">""" % (resname)
tinkerXmlFile.write( "%s\n" % (outputString) )
if resname == 'HOH':
tinkerXmlFile.write(f' <Residue name="{resname}" rigidWater="false">\n')
else:
tinkerXmlFile.write(f' <Residue name="{resname}">\n')
atomIndex = dict()
atomCount = 0
for atom in sorted( res['atoms'].keys() ):
......@@ -726,7 +728,7 @@ for resname, res in sorted(residueDict.items()):
for outputString in outputStrings:
tinkerXmlFile.write( "%s\n" % (outputString) )
tinkerXmlFile.write( " </Residue>\n" )
tinkerXmlFile.write( " </Residue>\n" )
# End caps
......
openmmapi/src/HarmonicBondForceImpl.cpp
View file @ edee11b6
......@@ -60,8 +60,6 @@ void HarmonicBondForceImpl::initialize(ContextImpl& context) {
}
if (length < 0)
throw OpenMMException("HarmonicBondForce: bond length cannot be negative");
if (k < 0)
throw OpenMMException("HarmonicBondForce: force constant cannot be negative");
}
kernel = context.getPlatform().createKernel(CalcHarmonicBondForceKernel::Name(), context);
kernel.getAs<CalcHarmonicBondForceKernel>().initialize(context.getSystem(), owner);
......
wrappers/python/openmm/app/data/amoeba2018.xml
View file @ edee11b6
<ForceField>
<Info>
<Source>amoebabio18.prm</Source>
<DateGenerated>2021-10-24</DateGenerated>
<DateGenerated>2021-11-02</DateGenerated>
<Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
<Reference>Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, Jay W Ponder, and Pengyu Ren. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. Journal of Chemical Theory and Computation, 14(4):2084-2108, 2018.</Reference>
</Info>
......@@ -393,7 +393,7 @@
<Bond from="3" to="8" />
<ExternalBond from="8" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="ARG">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -444,7 +444,7 @@
<Bond from="18" to="22" />
<ExternalBond from="19" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="ASH">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -473,7 +473,7 @@
<Bond from="8" to="12" />
<ExternalBond from="9" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="ASN">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -504,7 +504,7 @@
<Bond from="9" to="11" />
<ExternalBond from="10" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="ASP">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -531,7 +531,7 @@
<Bond from="4" to="8" />
<ExternalBond from="8" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="CALA">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -555,7 +555,7 @@
<Bond from="3" to="8" />
<Bond from="10" to="0" />
<ExternalBond from="8" />
</Residue>
</Residue>
<Residue name="CARG">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -607,7 +607,7 @@
<Bond from="18" to="22" />
<Bond from="24" to="0" />
<ExternalBond from="19" />
</Residue>
</Residue>
<Residue name="CASH">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -637,7 +637,7 @@
<Bond from="8" to="12" />
<Bond from="13" to="0" />
<ExternalBond from="9" />
</Residue>
</Residue>
<Residue name="CASN">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -669,7 +669,7 @@
<Bond from="9" to="11" />
<Bond from="14" to="0" />
<ExternalBond from="10" />
</Residue>
</Residue>
<Residue name="CASP">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -697,7 +697,7 @@
<Bond from="4" to="8" />
<Bond from="12" to="0" />
<ExternalBond from="8" />
</Residue>
</Residue>
<Residue name="CCYD">
<Atom name="C" type="233" />
<Atom name="CA" type="48" />
......@@ -721,7 +721,7 @@
<Bond from="3" to="7" />
<Bond from="9" to="0" />
<ExternalBond from="7" />
</Residue>
</Residue>
<Residue name="CCYS">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -747,7 +747,7 @@
<Bond from="7" to="11" />
<Bond from="10" to="0" />
<ExternalBond from="8" />
</Residue>
</Residue>
<Residue name="CCYX">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -772,7 +772,7 @@
<Bond from="9" to="0" />
<ExternalBond from="7" />
<ExternalBond from="10" />
</Residue>
</Residue>
<Residue name="CGLH">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -808,7 +808,7 @@
<Bond from="9" to="15" />
<Bond from="16" to="0" />
<ExternalBond from="12" />
</Residue>
</Residue>
<Residue name="CGLN">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -846,7 +846,7 @@
<Bond from="10" to="14" />
<Bond from="17" to="0" />
<ExternalBond from="13" />
</Residue>
</Residue>
<Residue name="CGLU">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -880,7 +880,7 @@
<Bond from="5" to="11" />
<Bond from="15" to="0" />
<ExternalBond from="11" />
</Residue>
</Residue>
<Residue name="CGLY">
<Atom name="C" type="233" />
<Atom name="CA" type="2" />
......@@ -898,7 +898,7 @@
<Bond from="2" to="5" />
<Bond from="7" to="0" />
<ExternalBond from="5" />
</Residue>
</Residue>
<Residue name="CHID">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -937,7 +937,7 @@
<Bond from="10" to="14" />
<Bond from="17" to="0" />
<ExternalBond from="13" />
</Residue>
</Residue>
<Residue name="CHIE">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -976,7 +976,7 @@
<Bond from="12" to="15" />
<Bond from="17" to="0" />
<ExternalBond from="13" />
</Residue>
</Residue>
<Residue name="CHIS">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1017,7 +1017,7 @@
<Bond from="13" to="16" />
<Bond from="18" to="0" />
<ExternalBond from="14" />
</Residue>
</Residue>
<Residue name="CILE">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1059,7 +1059,7 @@
<Bond from="6" to="17" />
<Bond from="19" to="0" />
<ExternalBond from="17" />
</Residue>
</Residue>
<Residue name="CLEU">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1101,7 +1101,7 @@
<Bond from="6" to="17" />
<Bond from="19" to="0" />
<ExternalBond from="17" />
</Residue>
</Residue>
<Residue name="CLYD">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1147,7 +1147,7 @@
<Bond from="17" to="19" />
<Bond from="21" to="0" />
<ExternalBond from="18" />
</Residue>
</Residue>
<Residue name="CLYS">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1195,7 +1195,7 @@
<Bond from="18" to="20" />
<Bond from="22" to="0" />
<ExternalBond from="19" />
</Residue>
</Residue>
<Residue name="CMET">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1233,7 +1233,7 @@
<Bond from="5" to="14" />
<Bond from="16" to="0" />
<ExternalBond from="14" />
</Residue>
</Residue>
<Residue name="CPHE">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1278,7 +1278,7 @@
<Bond from="9" to="18" />
<Bond from="20" to="0" />
<ExternalBond from="18" />
</Residue>
</Residue>
<Residue name="CPRO">
<Atom name="C" type="233" />
<Atom name="CA" type="51" />
......@@ -1311,7 +1311,7 @@
<Bond from="4" to="11" />
<Bond from="14" to="0" />
<ExternalBond from="12" />
</Residue>
</Residue>
<Residue name="CSER">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1337,7 +1337,7 @@
<Bond from="7" to="10" />
<Bond from="11" to="0" />
<ExternalBond from="8" />
</Residue>
</Residue>
<Residue name="CTHR">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1369,7 +1369,7 @@
<Bond from="7" to="13" />
<Bond from="14" to="0" />
<ExternalBond from="11" />
</Residue>
</Residue>
<Residue name="CTRP">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1423,7 +1423,7 @@
<Bond from="16" to="22" />
<Bond from="24" to="0" />
<ExternalBond from="21" />
</Residue>
</Residue>
<Residue name="CTYD">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1468,7 +1468,7 @@
<Bond from="9" to="17" />
<Bond from="20" to="0" />
<ExternalBond from="17" />
</Residue>
</Residue>
<Residue name="CTYR">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1515,7 +1515,7 @@
<Bond from="17" to="20" />
<Bond from="21" to="0" />
<ExternalBond from="18" />
</Residue>
</Residue>
<Residue name="CVAL">
<Atom name="C" type="233" />
<Atom name="CA" type="8" />
......@@ -1551,7 +1551,7 @@
<Bond from="5" to="14" />
<Bond from="16" to="0" />
<ExternalBond from="14" />
</Residue>
</Residue>
<Residue name="CYD">
<Atom name="C" type="9" />
<Atom name="CA" type="48" />
......@@ -1574,7 +1574,7 @@
<Bond from="3" to="7" />
<ExternalBond from="7" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="CYS">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -1599,7 +1599,7 @@
<Bond from="7" to="10" />
<ExternalBond from="8" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="CYX">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -1623,7 +1623,7 @@
<ExternalBond from="7" />
<ExternalBond from="0" />
<ExternalBond from="9" />
</Residue>
</Residue>
<Residue name="DA">
<Atom name="C1'" type="331" />
<Atom name="C2" type="254" />
......@@ -1693,7 +1693,7 @@
<Bond from="30" to="31" />
<ExternalBond from="31" />
<ExternalBond from="28" />
</Residue>
</Residue>
<Residue name="DA3">
<Atom name="C1'" type="331" />
<Atom name="C2" type="254" />
......@@ -1764,7 +1764,7 @@
<Bond from="28" to="32" />
<Bond from="31" to="32" />
<ExternalBond from="32" />
</Residue>
</Residue>
<Residue name="DA5">
<Atom name="C1'" type="331" />
<Atom name="C2" type="254" />
......@@ -1829,7 +1829,7 @@
<Bond from="19" to="24" />
<Bond from="20" to="24" />
<ExternalBond from="27" />
</Residue>
</Residue>
<Residue name="DAN">
<Atom name="C1'" type="331" />
<Atom name="C2" type="254" />
......@@ -1895,7 +1895,7 @@
<Bond from="19" to="30" />
<Bond from="20" to="25" />
<Bond from="21" to="25" />
</Residue>
</Residue>
<Residue name="DC">
<Atom name="C1'" type="331" />
<Atom name="C2" type="266" />
......@@ -1960,7 +1960,7 @@
<Bond from="28" to="29" />
<ExternalBond from="29" />
<ExternalBond from="26" />
</Residue>
</Residue>
<Residue name="DC3">
<Atom name="C1'" type="331" />
<Atom name="C2" type="266" />
......@@ -2026,7 +2026,7 @@
<Bond from="26" to="30" />
<Bond from="29" to="30" />
<ExternalBond from="30" />
</Residue>
</Residue>
<Residue name="DC5">
<Atom name="C1'" type="331" />
<Atom name="C2" type="266" />
......@@ -2086,7 +2086,7 @@
<Bond from="15" to="23" />
<Bond from="19" to="27" />
<ExternalBond from="25" />
</Residue>
</Residue>
<Residue name="DCN">
<Atom name="C1'" type="331" />
<Atom name="C2" type="266" />
......@@ -2147,7 +2147,7 @@
<Bond from="15" to="24" />
<Bond from="16" to="24" />
<Bond from="20" to="28" />
</Residue>
</Residue>
<Residue name="DG">
<Atom name="C1'" type="331" />
<Atom name="C2" type="273" />
......@@ -2219,7 +2219,7 @@
<Bond from="30" to="32" />
<ExternalBond from="32" />
<ExternalBond from="28" />
</Residue>
</Residue>
<Residue name="DG3">
<Atom name="C1'" type="331" />
<Atom name="C2" type="273" />
......@@ -2292,7 +2292,7 @@
<Bond from="28" to="33" />
<Bond from="31" to="33" />
<ExternalBond from="33" />
</Residue>
</Residue>
<Residue name="DG5">
<Atom name="C1'" type="331" />
<Atom name="C2" type="273" />
......@@ -2359,7 +2359,7 @@
<Bond from="15" to="23" />
<Bond from="20" to="29" />
<ExternalBond from="27" />
</Residue>
</Residue>
<Residue name="DGN">
<Atom name="C1'" type="331" />
<Atom name="C2" type="273" />
......@@ -2427,7 +2427,7 @@
<Bond from="15" to="24" />
<Bond from="17" to="28" />
<Bond from="21" to="30" />
</Residue>
</Residue>
<Residue name="DT">
<Atom name="C1'" type="331" />
<Atom name="C2" type="294" />
......@@ -2496,7 +2496,7 @@
<Bond from="30" to="31" />
<ExternalBond from="31" />
<ExternalBond from="27" />
</Residue>
</Residue>
<Residue name="DT3">
<Atom name="C1'" type="331" />
<Atom name="C2" type="294" />
......@@ -2566,7 +2566,7 @@
<Bond from="27" to="32" />
<Bond from="31" to="32" />
<ExternalBond from="32" />
</Residue>
</Residue>
<Residue name="DT5">
<Atom name="C1'" type="331" />
<Atom name="C2" type="294" />
......@@ -2630,7 +2630,7 @@
<Bond from="13" to="24" />
<Bond from="18" to="29" />
<ExternalBond from="26" />
</Residue>
</Residue>
<Residue name="DTN">
<Atom name="C1'" type="331" />
<Atom name="C2" type="294" />
......@@ -2695,7 +2695,7 @@
<Bond from="13" to="25" />
<Bond from="15" to="27" />
<Bond from="19" to="30" />
</Residue>
</Residue>
<Residue name="GLH">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -2730,7 +2730,7 @@
<Bond from="9" to="15" />
<ExternalBond from="12" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="GLN">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -2767,7 +2767,7 @@
<Bond from="10" to="14" />
<ExternalBond from="13" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="GLU">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -2800,7 +2800,7 @@
<Bond from="5" to="11" />
<ExternalBond from="11" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="GLY">
<Atom name="C" type="3" />
<Atom name="CA" type="2" />
......@@ -2817,7 +2817,7 @@
<Bond from="2" to="5" />
<ExternalBond from="5" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="HID">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -2855,7 +2855,7 @@
<Bond from="10" to="14" />
<ExternalBond from="13" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="HIE">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -2893,7 +2893,7 @@
<Bond from="12" to="15" />
<ExternalBond from="13" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="HIS">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -2933,14 +2933,14 @@
<Bond from="13" to="16" />
<ExternalBond from="14" />
<ExternalBond from="0" />
</Residue>
<Residue name="HOH">
</Residue>
<Residue name="HOH" rigidWater="false">
<Atom name="H1" type="350" />
<Atom name="H2" type="350" />
<Atom name="O" type="349" />
<Bond from="0" to="2" />
<Bond from="1" to="2" />
</Residue>
</Residue>
<Residue name="ILE">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -2981,7 +2981,7 @@
<Bond from="6" to="17" />
<ExternalBond from="17" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="LEU">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3022,7 +3022,7 @@
<Bond from="6" to="17" />
<ExternalBond from="17" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="LYD">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3067,7 +3067,7 @@
<Bond from="17" to="19" />
<ExternalBond from="18" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="LYS">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3114,7 +3114,7 @@
<Bond from="18" to="20" />
<ExternalBond from="19" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="MET">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3151,7 +3151,7 @@
<Bond from="5" to="14" />
<ExternalBond from="14" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NALA">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3177,7 +3177,7 @@
<Bond from="4" to="10" />
<Bond from="5" to="10" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NARG">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3231,7 +3231,7 @@
<Bond from="19" to="24" />
<Bond from="20" to="24" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NASH">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3263,7 +3263,7 @@
<Bond from="6" to="11" />
<Bond from="10" to="14" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NASN">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3297,7 +3297,7 @@
<Bond from="10" to="13" />
<Bond from="11" to="13" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NASP">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3327,7 +3327,7 @@
<Bond from="5" to="10" />
<Bond from="6" to="10" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NCYD">
<Atom name="C" type="9" />
<Atom name="CA" type="48" />
......@@ -3353,7 +3353,7 @@
<Bond from="4" to="9" />
<Bond from="5" to="9" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NCYS">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3381,7 +3381,7 @@
<Bond from="5" to="10" />
<Bond from="9" to="12" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NCYX">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3408,7 +3408,7 @@
<Bond from="5" to="9" />
<ExternalBond from="0" />
<ExternalBond from="11" />
</Residue>
</Residue>
<Residue name="NGLH">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3446,7 +3446,7 @@
<Bond from="7" to="14" />
<Bond from="11" to="17" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NGLN">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3486,7 +3486,7 @@
<Bond from="11" to="16" />
<Bond from="12" to="16" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NGLU">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3522,7 +3522,7 @@
<Bond from="6" to="13" />
<Bond from="7" to="13" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NGLY">
<Atom name="C" type="3" />
<Atom name="CA" type="2" />
......@@ -3542,7 +3542,7 @@
<Bond from="3" to="7" />
<Bond from="4" to="7" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NHID">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3583,7 +3583,7 @@
<Bond from="8" to="15" />
<Bond from="12" to="16" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NHIE">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3624,7 +3624,7 @@
<Bond from="8" to="15" />
<Bond from="14" to="17" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NHIS">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3667,7 +3667,7 @@
<Bond from="12" to="17" />
<Bond from="15" to="18" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NILE">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3711,7 +3711,7 @@
<Bond from="7" to="19" />
<Bond from="8" to="19" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NLEU">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3755,7 +3755,7 @@
<Bond from="7" to="19" />
<Bond from="8" to="19" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NLYD">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3803,7 +3803,7 @@
<Bond from="18" to="21" />
<Bond from="19" to="21" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NLYS">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3853,7 +3853,7 @@
<Bond from="19" to="22" />
<Bond from="20" to="22" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NMET">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3893,7 +3893,7 @@
<Bond from="6" to="16" />
<Bond from="7" to="16" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NPHE">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -3940,7 +3940,7 @@
<Bond from="10" to="20" />
<Bond from="11" to="20" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NPRO">
<Atom name="C" type="242" />
<Atom name="CA" type="241" />
......@@ -3975,7 +3975,7 @@
<Bond from="5" to="14" />
<Bond from="6" to="14" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NSER">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -4003,7 +4003,7 @@
<Bond from="5" to="10" />
<Bond from="9" to="12" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NTHR">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -4037,7 +4037,7 @@
<Bond from="6" to="13" />
<Bond from="9" to="15" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NTRP">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -4093,7 +4093,7 @@
<Bond from="13" to="23" />
<Bond from="18" to="24" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NTYD">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -4140,7 +4140,7 @@
<Bond from="10" to="19" />
<Bond from="11" to="19" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NTYR">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -4189,7 +4189,7 @@
<Bond from="11" to="20" />
<Bond from="19" to="22" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="NVAL">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -4227,7 +4227,7 @@
<Bond from="6" to="16" />
<Bond from="7" to="16" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="PHE">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -4271,7 +4271,7 @@
<Bond from="9" to="18" />
<ExternalBond from="18" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="PRO">
<Atom name="C" type="52" />
<Atom name="CA" type="51" />
......@@ -4303,7 +4303,7 @@
<Bond from="4" to="11" />
<ExternalBond from="12" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="RA">
<Atom name="C1'" type="314" />
<Atom name="C2" type="254" />
......@@ -4375,7 +4375,7 @@
<Bond from="31" to="32" />
<ExternalBond from="32" />
<ExternalBond from="29" />
</Residue>
</Residue>
<Residue name="RA3">
<Atom name="C1'" type="314" />
<Atom name="C2" type="254" />
......@@ -4448,7 +4448,7 @@
<Bond from="29" to="33" />
<Bond from="32" to="33" />
<ExternalBond from="33" />
</Residue>
</Residue>
<Residue name="RA5">
<Atom name="C1'" type="314" />
<Atom name="C2" type="254" />
......@@ -4515,7 +4515,7 @@
<Bond from="19" to="24" />
<Bond from="21" to="27" />
<ExternalBond from="28" />
</Residue>
</Residue>
<Residue name="RAN">
<Atom name="C1'" type="314" />
<Atom name="C2" type="254" />
......@@ -4583,7 +4583,7 @@
<Bond from="19" to="25" />
<Bond from="20" to="25" />
<Bond from="22" to="28" />
</Residue>
</Residue>
<Residue name="RC">
<Atom name="C1'" type="314" />
<Atom name="C2" type="266" />
......@@ -4650,7 +4650,7 @@
<Bond from="29" to="30" />
<ExternalBond from="30" />
<ExternalBond from="27" />
</Residue>
</Residue>
<Residue name="RC3">
<Atom name="C1'" type="314" />
<Atom name="C2" type="266" />
......@@ -4718,7 +4718,7 @@
<Bond from="27" to="31" />
<Bond from="30" to="31" />
<ExternalBond from="31" />
</Residue>
</Residue>
<Residue name="RC5">
<Atom name="C1'" type="314" />
<Atom name="C2" type="266" />
......@@ -4780,7 +4780,7 @@
<Bond from="18" to="28" />
<Bond from="20" to="25" />
<ExternalBond from="26" />
</Residue>
</Residue>
<Residue name="RCN">
<Atom name="C1'" type="314" />
<Atom name="C2" type="266" />
......@@ -4843,7 +4843,7 @@
<Bond from="15" to="24" />
<Bond from="19" to="29" />
<Bond from="21" to="26" />
</Residue>
</Residue>
<Residue name="RG">
<Atom name="C1'" type="314" />
<Atom name="C2" type="273" />
......@@ -4917,7 +4917,7 @@
<Bond from="31" to="33" />
<ExternalBond from="33" />
<ExternalBond from="29" />
</Residue>
</Residue>
<Residue name="RG3">
<Atom name="C1'" type="314" />
<Atom name="C2" type="273" />
......@@ -4992,7 +4992,7 @@
<Bond from="29" to="34" />
<Bond from="32" to="34" />
<ExternalBond from="34" />
</Residue>
</Residue>
<Residue name="RG5">
<Atom name="C1'" type="314" />
<Atom name="C2" type="273" />
......@@ -5061,7 +5061,7 @@
<Bond from="19" to="30" />
<Bond from="21" to="27" />
<ExternalBond from="28" />
</Residue>
</Residue>
<Residue name="RGN">
<Atom name="C1'" type="314" />
<Atom name="C2" type="273" />
......@@ -5131,7 +5131,7 @@
<Bond from="16" to="29" />
<Bond from="20" to="31" />
<Bond from="22" to="28" />
</Residue>
</Residue>
<Residue name="RU">
<Atom name="C1'" type="314" />
<Atom name="C2" type="300" />
......@@ -5196,7 +5196,7 @@
<Bond from="28" to="29" />
<ExternalBond from="29" />
<ExternalBond from="25" />
</Residue>
</Residue>
<Residue name="RU3">
<Atom name="C1'" type="314" />
<Atom name="C2" type="300" />
......@@ -5262,7 +5262,7 @@
<Bond from="25" to="30" />
<Bond from="29" to="30" />
<ExternalBond from="30" />
</Residue>
</Residue>
<Residue name="RU5">
<Atom name="C1'" type="314" />
<Atom name="C2" type="300" />
......@@ -5322,7 +5322,7 @@
<Bond from="17" to="27" />
<Bond from="19" to="23" />
<ExternalBond from="24" />
</Residue>
</Residue>
<Residue name="RUN">
<Atom name="C1'" type="314" />
<Atom name="C2" type="300" />
......@@ -5383,7 +5383,7 @@
<Bond from="13" to="25" />
<Bond from="18" to="28" />
<Bond from="20" to="24" />
</Residue>
</Residue>
<Residue name="SER">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -5408,7 +5408,7 @@
<Bond from="7" to="10" />
<ExternalBond from="8" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="THR">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -5439,7 +5439,7 @@
<Bond from="7" to="13" />
<ExternalBond from="11" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="TRP">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -5492,7 +5492,7 @@
<Bond from="16" to="22" />
<ExternalBond from="21" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="TYD">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -5536,7 +5536,7 @@
<Bond from="9" to="17" />
<ExternalBond from="17" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="TYR">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -5582,7 +5582,7 @@
<Bond from="17" to="20" />
<ExternalBond from="18" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="VAL">
<Atom name="C" type="9" />
<Atom name="CA" type="8" />
......@@ -5617,7 +5617,7 @@
<Bond from="5" to="14" />
<ExternalBond from="14" />
<ExternalBond from="0" />
</Residue>
</Residue>
<Residue name="ACE">
<Atom name="HH31" type="222"/>
<Atom name="CH3" type="221"/>
......
wrappers/python/openmm/app/data/amoeba2018_gk.xml
View file @ edee11b6
<ForceField>
<Info>
<Source>amoebabio18.prm</Source>
<DateGenerated>2021-10-24</DateGenerated>
<DateGenerated>2021-11-02</DateGenerated>
<Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
<Reference>Rae A. Corrigan, Guowei Qi, Andrew C. Thiel, Jack R. Lynn, Brandon D. Walker, Thomas L. Casavant, Louis Lagardere, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Ren, and Michael J. Schnieders. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation, 17(4):2323-2341, 2021.</Reference>
</Info>
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment