Added data files that missed getting checked in

wrappers/python/simtk/openmm/app/data/pdbNames.xml

+<Residues>
+ <Residue name="All">
+ </Residue>
+ <Residue name="Protein">
+  <Atom name="H" alt1="HN" alt2="H1" alt3="1H" alt4="HN1" alt5="HT1"/>
+  <Atom name="H2" alt1="2H" alt2="HN2" alt3="HT2"/>
+  <Atom name="H3" alt1="3H" alt2="HN3" alt3="HT3"/>
+  <Atom name="O" alt1="O1" alt2="OT1" alt3="OCT1" alt4="OC1"/>
+  <Atom name="OXT" alt1="O2" alt2="OT2" alt3="OCT2" alt4="OC2" alt5="OT"/>
+ </Residue>
+ <Residue name="Nucleic">
+  <Atom name="H" alt1="HN"/>
+  <Atom name="OP1" alt1="O1P"/>
+  <Atom name="OP2" alt1="O2P"/>
+  <Atom name="OP3" alt1="O3P"/>
+  <Atom name="HOP2" alt1="2HOP"/>
+  <Atom name="HOP3" alt1="3HOP"/>
+  <Atom name="C1'" alt1="C1*"/>
+  <Atom name="C2'" alt1="C2*"/>
+  <Atom name="C3'" alt1="C3*"/>
+  <Atom name="C4'" alt1="C4*"/>
+  <Atom name="C5'" alt1="C5*"/>
+  <Atom name="O2'" alt1="O2*"/>
+  <Atom name="O3'" alt1="O3*"/>
+  <Atom name="O4'" alt1="O4*"/>
+  <Atom name="O5'" alt1="O5*"/>
+  <Atom name="H1'" alt1="H1*"/>
+  <Atom name="H2'" alt1="H2*" alt2="1H2*"/>
+  <Atom name="H2''" alt1="2H2*"/>
+  <Atom name="H3'" alt1="H3*"/>
+  <Atom name="H4'" alt1="H4*"/>
+  <Atom name="H5'" alt1="1H5*"/>
+  <Atom name="H5''" alt1="2H5*"/>
+  <Atom name="HO2'" alt1="2HO*"/>
+  <Atom name="HO3'" alt1="H3T"/>
+ </Residue>
+ <Residue name="GLY" type="Protein">
+  <Atom name="HA2" alt1="2HA"/>
+  <Atom name="HA3" alt1="HA1" alt2="1HA" alt3="3HA"/>
+ </Residue>
+ <Residue name="ALA" type="Protein">
+  <Atom name="HB1" alt1="1HB"/>
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="3HB"/>
+ </Residue>
+ <Residue name="VAL" type="Protein">
+  <Atom name="HG11" alt1="1HG1"/>
+  <Atom name="HG12" alt1="2HG1"/>
+  <Atom name="HG13" alt1="3HG1"/>
+  <Atom name="HG21" alt1="1HG2"/>
+  <Atom name="HG22" alt1="2HG2"/>
+  <Atom name="HG23" alt1="3HG2"/>
+ </Residue>
+ <Residue name="LEU" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HD11" alt1="1HD1"/>
+  <Atom name="HD12" alt1="2HD1"/>
+  <Atom name="HD13" alt1="3HD1"/>
+  <Atom name="HD21" alt1="1HD2"/>
+  <Atom name="HD22" alt1="2HD2"/>
+  <Atom name="HD23" alt1="3HD2"/>
+ </Residue>
+ <Residue name="ILE" type="Protein">
+  <Atom name="CD1" alt1="CD"/>
+  <Atom name="HG12" alt1="2HG1"/>
+  <Atom name="HG13" alt1="HG11" alt2="1HG1" alt3="3HG1"/>
+  <Atom name="HG21" alt1="1HG2"/>
+  <Atom name="HG22" alt1="2HG2"/>
+  <Atom name="HG23" alt1="3HG2"/>
+  <Atom name="HD11" alt1="1HD1" alt2="HD1"/>
+  <Atom name="HD12" alt1="2HD1" alt2="HD2"/>
+  <Atom name="HD13" alt1="3HD1" alt2="HD3"/>
+ </Residue>
+ <Residue name="SER" type="Protein">
+  <Atom name="OG" alt1="OG1"/>
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG" alt1="HG1" alt2="HOG"/>
+ </Residue>
+ <Residue name="THR" type="Protein">
+  <Atom name="OG1" alt1="OG"/>
+  <Atom name="CG2" alt1="CG"/>
+  <Atom name="HG1" alt1="HOG" alt2="HOG1" alt3="1HG"/>
+  <Atom name="HG21" alt1="1HG2"/>
+  <Atom name="HG22" alt1="2HG2"/>
+  <Atom name="HG23" alt1="3HG2"/>
+ </Residue>
+ <Residue name="CYS" type="Protein" alt1="CYX">
+  <Atom name="SG" alt1="SG1"/>
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG" alt1="HG1" alt2="HSG"/>
+ </Residue>
+ <Residue name="PRO" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+  <Atom name="HD2" alt1="2HD"/>
+  <Atom name="HD3" alt1="HD1" alt2="1HD" alt3="3HD"/>
+  <Atom name="H2" alt1="HT1"/>
+  <Atom name="H3" alt1="HT2"/>
+ </Residue>
+ <Residue name="PHE" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+ </Residue>
+ <Residue name="TYR" type="Protein">
+  <Atom name="HH" alt1="HOH"/>
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+ </Residue>
+ <Residue name="TRP" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HE1" alt1="HNE"/>
+ </Residue>
+ <Residue name="HIS" type="Protein" alt1="HSP" alt2="HSH" alt3="HIP" alt4="HIH" alt5="HID" alt6="HIE">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HD1" alt1="HND" alt2="HND1"/>
+  <Atom name="HD2" alt1="HD"/>
+  <Atom name="HE1" alt1="HE"/>
+  <Atom name="HE2" alt1="HNE" alt2="HNE2"/>
+ </Residue>
+ <Residue name="ASP" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+ </Residue>
+ <Residue name="ASN" type="Protein">
+  <Atom name="OD1" alt1="OD"/>
+  <Atom name="ND2" alt1="ND"/>
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HD21" alt1="1HD2" alt2="HND1"/>
+  <Atom name="HD22" alt1="2HD2" alt2="HND2"/>
+ </Residue>
+ <Residue name="GLU" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+ </Residue>
+ <Residue name="GLN" type="Protein">
+  <Atom name="OE1" alt1="OE"/>
+  <Atom name="NE2" alt1="NE"/>
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+  <Atom name="HE21" alt1="1HE2" alt2="HNE1"/>
+  <Atom name="HE22" alt1="2HE2" alt2="HNE2"/>
+ </Residue>
+ <Residue name="MET" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+  <Atom name="HE1" alt1="1HE"/>
+  <Atom name="HE2" alt1="2HE"/>
+  <Atom name="HE3" alt1="3HE"/>
+ </Residue>
+ <Residue name="LYS" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+  <Atom name="HD2" alt1="2HD"/>
+  <Atom name="HD3" alt1="HD1" alt2="1HD" alt3="3HD"/>
+  <Atom name="HE2" alt1="2HE"/>
+  <Atom name="HE3" alt1="HE1" alt2="1HE" alt3="3HE"/>
+  <Atom name="HZ1" alt1="1HZ" alt2="HNZ1"/>
+  <Atom name="HZ2" alt1="2HZ" alt2="HNZ2"/>
+  <Atom name="HZ3" alt1="3HZ" alt2="HNZ3"/>
+ </Residue>
+ <Residue name="ARG" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+  <Atom name="HD2" alt1="2HD"/>
+  <Atom name="HD3" alt1="HD1" alt2="1HD" alt3="3HD"/>
+  <Atom name="HH11" alt1="1HH1" alt2="HN11"/>
+  <Atom name="HH12" alt1="2HH1" alt2="HN12"/>
+  <Atom name="HH21" alt1="1HH2" alt2="HN21"/>
+  <Atom name="HH22" alt1="2HH2" alt2="HN22"/>
+ </Residue>
+ <Residue name="ORN" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+  <Atom name="HD2" alt1="2HD"/>
+  <Atom name="HD3" alt1="HD1" alt2="1HD" alt3="3HD"/>
+  <Atom name="HE1" alt1="1HE" alt2="HNE1"/>
+  <Atom name="HE2" alt1="2HE" alt2="HNE2"/>
+  <Atom name="HE3" alt1="3HE" alt2="HNE3"/>
+ </Residue>
+ <Residue name="AIB" type="Protein">
+  <Atom name="HB11" alt1="1HB1"/>
+  <Atom name="HB12" alt1="2HB1"/>
+  <Atom name="HB13" alt1="3HB1"/>
+  <Atom name="HB21" alt1="1HB2"/>
+  <Atom name="HB22" alt1="2HB2"/>
+  <Atom name="HB23" alt1="3HB2"/>
+ </Residue>
+ <Residue name="PCA" type="Protein">
+  <Atom name="HB2" alt1="2HB"/>
+  <Atom name="HB3" alt1="HB1" alt2="1HB" alt3="3HB"/>
+  <Atom name="HG2" alt1="2HG"/>
+  <Atom name="HG3" alt1="HG1" alt2="1HG" alt3="3HG"/>
+ </Residue>
+ <Residue name="FOR" type="Protein">
+  <Atom name="C" alt1="CY"/>
+  <Atom name="O" alt1="OY"/>
+  <Atom name="H" alt1="HY"/>
+ </Residue>
+ <Residue name="ACE" type="Protein">
+  <Atom name="C" alt1="CY"/>
+  <Atom name="CH3" alt1="CAY" alt2="CA"/>
+  <Atom name="O" alt1="OY"/>
+  <Atom name="H1" alt1="1H" alt2="HY1" alt3="HH31" alt4="1HH3"/>
+  <Atom name="H2" alt1="2H" alt2="HY2" alt3="HH32" alt4="2HH3"/>
+  <Atom name="H3" alt1="3H" alt2="HY3" alt3="HH33" alt4="3HH3"/>
+ </Residue>
+ <Residue name="NME" alt1="NMA" type="Protein">
+  <Atom name="N" alt1="NT"/>
+  <Atom name="C" alt1="CH3" alt2="CT" alt3="CAT" alt4="CA"/>
+  <Atom name="H" alt1="HNT" alt2="HN"/>
+  <Atom name="H1" alt1="1H" alt2="1HA" alt3="HT1" alt4="HH31" alt5="1HH3"/>
+  <Atom name="H2" alt1="2H" alt2="2HA" alt3="HT2" alt4="HH32" alt5="2HH3"/>
+  <Atom name="H3" alt1="3H" alt2="3HA" alt3="HT3" alt4="HH33" alt5="3HH3"/>
+ </Residue>
+ <Residue name="NH2" type="Protein">
+  <Atom name="N" alt1="NT"/>
+  <Atom name="H1" alt1="1H" alt2="HT1"/>
+  <Atom name="H2" alt1="2H" alt2="HT2"/>
+ </Residue>
+ <Residue name="UNK" type="Protein"/>
+ <Residue name="A" alt1="ADE" type="Nucleic">
+  <Atom name="H61" alt1="1H6"/>
+  <Atom name="H62" alt1="2H6"/>
+ </Residue>
+ <Residue name="G" alt1="GUA" type="Nucleic">
+  <Atom name="H21" alt1="1H2"/>
+  <Atom name="H22" alt1="2H2"/>
+ </Residue>
+ <Residue name="C" alt1="CYT" type="Nucleic">
+  <Atom name="H41" alt1="1H4"/>
+  <Atom name="H42" alt1="2H4"/>
+ </Residue>
+ <Residue name="U" alt1="URA" type="Nucleic"/>
+ <Residue name="DA" alt1="DAD" type="Nucleic">
+  <Atom name="H61" alt1="1H6"/>
+  <Atom name="H62" alt1="2H6"/>
+ </Residue>
+ <Residue name="DG" alt1="DGU" type="Nucleic">
+  <Atom name="H21" alt1="1H2"/>
+  <Atom name="H22" alt1="2H2"/>
+ </Residue>
+ <Residue name="DC" alt1="DCY" type="Nucleic">
+  <Atom name="H41" alt1="1H4"/>
+  <Atom name="H42" alt1="2H4"/>
+ </Residue>
+ <Residue name="DT" alt1="THY" type="Nucleic">
+  <Atom name="C7" alt1="C5M"/>
+  <Atom name="H71" alt1="1H5M"/>
+  <Atom name="H72" alt1="2H5M"/>
+  <Atom name="H73" alt1="3H5M"/>
+ </Residue>
+ <Residue name="HOH" alt1="H20" alt2="WAT">
+  <Atom name="O" alt1="OW"/>
+  <Atom name="H1" alt1="HW1"/>
+  <Atom name="H2" alt1="HW2"/>
+ </Residue>
+</Residues>

wrappers/python/simtk/openmm/app/data/spce.xml

+<ForceField>
+ <AtomTypes>
+  <Type name="spce-O" class="OW" element="O" mass="15.99943"/>
+  <Type name="spce-H" class="HW" element="H" mass="1.007947"/>
+ </AtomTypes>
+ <Residues>
+  <Residue name="HOH">
+   <Atom name="O" type="spce-O"/>
+   <Atom name="H1" type="spce-H"/>
+   <Atom name="H2" type="spce-H"/>
+   <Bond from="0" to="1"/>
+   <Bond from="0" to="2"/>
+  </Residue>
+ </Residues>
+ <HarmonicBondForce>
+  <Bond class1="OW" class2="HW" length="0.1" k="462750.4"/>
+ </HarmonicBondForce>
+ <HarmonicAngleForce>
+  <Angle class1="HW" class2="OW" class3="HW" angle="1.91061193216" k="836.8"/>
+ </HarmonicAngleForce>
+ <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+  <Atom type="spce-O" charge="-0.8476" sigma="0.31657195050398818" epsilon="0.6497752"/>
+  <Atom type="spce-H" charge="0.4238" sigma="1" epsilon="0"/>
+ </NonbondedForce>
+</ForceField>
+