Fix errors with AMOEBA 2018 (#3311)

devtools/forcefield-scripts/processTinkerForceField.py

@@ -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() ):

openmmapi/src/HarmonicBondForceImpl.cpp

@@ -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

 <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>
@@ -2934,7 +2934,7 @@
    <ExternalBond from="14" />
    <ExternalBond from="0" />
   </Residue>
-  <Residue name="HOH">
+  <Residue name="HOH" rigidWater="false">
    <Atom name="H1" type="350" />
    <Atom name="H2" type="350" />
    <Atom name="O" type="349" />

wrappers/python/openmm/app/data/amoeba2018_gk.xml

 <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>