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Commit 245a7380 authored by Jason Swails's avatar Jason Swails
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Merge branch 'master' of https://github.com/pandegroup/openmm

parents fd1827e0 b43e3f12
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devtools/forcefield-scripts/residuesFinal.xml 0 → 100644
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<Residues>
<Residue abbreviation="ALA" loc="middle" type="protein" tinkerLookupName="Alanine" fullName="Alanine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB1" tinkerLookupName="HB" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="HB1" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="ARG" loc="middle" type="protein" tinkerLookupName="Arginine" fullName="Arginine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD" tinkerLookupName="CD" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="CZ" tinkerLookupName="CZ" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD" bonds="1" />
<Atom name="HD3" tinkerLookupName="HD" bonds="1" />
<Atom name="HE" tinkerLookupName="HE" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="HH11" tinkerLookupName="HH" bonds="1" />
<Atom name="HH12" tinkerLookupName="HH" bonds="1" />
<Atom name="HH21" tinkerLookupName="HH" bonds="1" />
<Atom name="HH22" tinkerLookupName="HH" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="NE" tinkerLookupName="NE" bonds="3" />
<Atom name="NH1" tinkerLookupName="NH" bonds="3" />
<Atom name="NH2" tinkerLookupName="NH" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD" to="HD3" />
<Bond from="CD" to="CG" />
<Bond from="CD" to="NE" />
<Bond from="CD" to="HD2" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
<Bond from="CZ" to="NH1" />
<Bond from="CZ" to="NE" />
<Bond from="CZ" to="NH2" />
<Bond from="H" to="N" />
<Bond from="HE" to="NE" />
<Bond from="HH11" to="NH1" />
<Bond from="HH12" to="NH1" />
<Bond from="HH21" to="NH2" />
<Bond from="HH22" to="NH2" />
</Residue>
<Residue abbreviation="ASN" loc="middle" type="protein" tinkerLookupName="Asparagine" fullName="Asparagine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD21" tinkerLookupName="HD2" bonds="1" />
<Atom name="HD22" tinkerLookupName="HD2" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="ND2" tinkerLookupName="ND2" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OD1" tinkerLookupName="OD1" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CG" to="ND2" />
<Bond from="CG" to="OD1" />
<Bond from="H" to="N" />
<Bond from="HD21" to="ND2" />
<Bond from="HD22" to="ND2" />
</Residue>
<Residue abbreviation="ASP" loc="middle" type="protein" tinkerLookupName="Aspartic Acid" fullName="Aspartic Acid">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OD1" tinkerLookupName="OD" bonds="1" />
<Atom name="OD2" tinkerLookupName="OD" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CG" to="OD2" />
<Bond from="CG" to="OD1" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="ASH" loc="middle" type="protein" tinkerLookupName="Aspartic Acid (COOH)" fullName="Aspartic Acid">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD2" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OD1" tinkerLookupName="OD1" bonds="1" />
<Atom name="OD2" tinkerLookupName="OD2" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CG" to="OD2" />
<Bond from="CG" to="OD1" />
<Bond from="H" to="N" />
<Bond from="HD2" to="OD2" />
</Residue>
<Residue abbreviation="CYS" loc="middle" type="protein" tinkerLookupName="Cysteine (SH)" fullName="Cysteine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HG" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="SG" tinkerLookupName="SG" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="SG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="H" to="N" />
<Bond from="HG" to="SG" />
</Residue>
<Residue abbreviation="CYD" loc="middle" type="protein" tinkerLookupName="Cysteine (S-)" fullName="Cysteine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="SG" tinkerLookupName="SG" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="SG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="CYX" loc="middle" type="protein" tinkerLookupName="Cystine (SS)" fullName="Cystine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="SG" tinkerLookupName="SG" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="SG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="GLN" loc="middle" type="protein" tinkerLookupName="Glutamine" fullName="Glutamine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD" tinkerLookupName="CD" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HE21" tinkerLookupName="HE2" bonds="1" />
<Atom name="HE22" tinkerLookupName="HE2" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="NE2" tinkerLookupName="NE2" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OE1" tinkerLookupName="OE1" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD" to="NE2" />
<Bond from="CD" to="OE1" />
<Bond from="CD" to="CG" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
<Bond from="H" to="N" />
<Bond from="HE21" to="NE2" />
<Bond from="HE22" to="NE2" />
</Residue>
<Residue abbreviation="GLU" loc="middle" type="protein" tinkerLookupName="Glutamic Acid" fullName="Glutamic Acid">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD" tinkerLookupName="CD" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OE1" tinkerLookupName="OE" bonds="1" />
<Atom name="OE2" tinkerLookupName="OE" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD" to="OE2" />
<Bond from="CD" to="OE1" />
<Bond from="CD" to="CG" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="GLH" loc="middle" type="protein" tinkerLookupName="Glutamic Acid (COOH)" fullName="Glutamic Acid">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD" tinkerLookupName="CD" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE2" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OE1" tinkerLookupName="OE1" bonds="1" />
<Atom name="OE2" tinkerLookupName="OE2" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD" to="OE2" />
<Bond from="CD" to="OE1" />
<Bond from="CD" to="CG" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
<Bond from="H" to="N" />
<Bond from="HE2" to="OE2" />
</Residue>
<Residue abbreviation="GLY" loc="middle" type="protein" tinkerLookupName="Glycine" fullName="Glycine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA2" tinkerLookupName="HA" bonds="1" />
<Atom name="HA3" tinkerLookupName="HA" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="HA3" />
<Bond from="CA" to="HA2" />
<Bond from="CA" to="N" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="HIS" loc="middle" type="protein" tinkerLookupName="Histidine (+)" fullName="Histidine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD2" tinkerLookupName="CD2" bonds="3" />
<Atom name="CE1" tinkerLookupName="CE1" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD1" tinkerLookupName="HD1" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD2" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE1" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE2" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="ND1" tinkerLookupName="ND1" bonds="3" />
<Atom name="NE2" tinkerLookupName="NE2" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="NE2" />
<Bond from="CD2" to="HD2" />
<Bond from="CE1" to="ND1" />
<Bond from="CE1" to="NE2" />
<Bond from="CE1" to="HE1" />
<Bond from="CG" to="ND1" />
<Bond from="H" to="N" />
<Bond from="HD1" to="ND1" />
<Bond from="HD2" to="CD2" />
<Bond from="HE2" to="NE2" />
</Residue>
<Residue abbreviation="HID" loc="middle" type="protein" tinkerLookupName="Histidine (HD)" fullName="Histidine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD2" tinkerLookupName="CD2" bonds="3" />
<Atom name="CE1" tinkerLookupName="CE1" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD1" tinkerLookupName="HD1" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD2" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE1" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="ND1" tinkerLookupName="ND1" bonds="3" />
<Atom name="NE2" tinkerLookupName="NE2" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="NE2" />
<Bond from="CD2" to="HD2" />
<Bond from="CE1" to="ND1" />
<Bond from="CE1" to="NE2" />
<Bond from="CE1" to="HE1" />
<Bond from="CG" to="ND1" />
<Bond from="H" to="N" />
<Bond from="HD1" to="ND1" />
</Residue>
<Residue abbreviation="HIE" loc="middle" type="protein" tinkerLookupName="Histidine (HE)" fullName="Histidine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD2" tinkerLookupName="CD2" bonds="3" />
<Atom name="CE1" tinkerLookupName="CE1" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD2" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE1" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE2" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="ND1" tinkerLookupName="ND1" bonds="3" />
<Atom name="NE2" tinkerLookupName="NE2" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="NE2" />
<Bond from="CD2" to="HD2" />
<Bond from="CE1" to="ND1" />
<Bond from="CE1" to="NE2" />
<Bond from="CE1" to="HE1" />
<Bond from="CG" to="ND1" />
<Bond from="H" to="N" />
<Bond from="HE2" to="NE2" />
</Residue>
<Residue abbreviation="HOH" loc="middle" type="AmoebaWater" tinkerLookupName="Water" fullName="Water">
<Atom name="H1" tinkerLookupName="H" bonds="1" />
<Atom name="H2" tinkerLookupName="H" bonds="1" />
<Atom name="O" tinkerLookupName="O" bonds="2" />
<Bond from="O" to="H1" />
<Bond from="O" to="H2" />
</Residue>
<Residue abbreviation="ILE" loc="middle" type="protein" tinkerLookupName="Isoleucine" fullName="Isoleucine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD1" tinkerLookupName="CD" bonds="4" />
<Atom name="CG1" tinkerLookupName="CG1" bonds="4" />
<Atom name="CG2" tinkerLookupName="CG2" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB" tinkerLookupName="HB" bonds="1" />
<Atom name="HD11" tinkerLookupName="HD" bonds="1" />
<Atom name="HD12" tinkerLookupName="HD" bonds="1" />
<Atom name="HD13" tinkerLookupName="HD" bonds="1" />
<Atom name="HG12" tinkerLookupName="HG1" bonds="1" />
<Atom name="HG13" tinkerLookupName="HG1" bonds="1" />
<Atom name="HG21" tinkerLookupName="HG2" bonds="1" />
<Atom name="HG22" tinkerLookupName="HG2" bonds="1" />
<Atom name="HG23" tinkerLookupName="HG2" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG1" />
<Bond from="CB" to="HB" />
<Bond from="CB" to="CG2" />
<Bond from="CD1" to="CG1" />
<Bond from="CD1" to="HD12" />
<Bond from="CD1" to="HD11" />
<Bond from="CD1" to="HD13" />
<Bond from="CG1" to="HG12" />
<Bond from="CG1" to="HG13" />
<Bond from="CG2" to="HG21" />
<Bond from="CG2" to="HG23" />
<Bond from="CG2" to="HG22" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="LEU" loc="middle" type="protein" tinkerLookupName="Leucine" fullName="Leucine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD1" tinkerLookupName="CD1" bonds="4" />
<Atom name="CD2" tinkerLookupName="CD2" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD11" tinkerLookupName="HD1" bonds="1" />
<Atom name="HD12" tinkerLookupName="HD1" bonds="1" />
<Atom name="HD13" tinkerLookupName="HD1" bonds="1" />
<Atom name="HD21" tinkerLookupName="HD2" bonds="1" />
<Atom name="HD22" tinkerLookupName="HD2" bonds="1" />
<Atom name="HD23" tinkerLookupName="HD2" bonds="1" />
<Atom name="HG" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD1" to="HD13" />
<Bond from="CD1" to="HD12" />
<Bond from="CD1" to="HD11" />
<Bond from="CD1" to="CG" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="HD22" />
<Bond from="CD2" to="HD23" />
<Bond from="CD2" to="HD21" />
<Bond from="CG" to="HG" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="LYS" loc="middle" type="protein" tinkerLookupName="Lysine" fullName="Lysine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD" tinkerLookupName="CD" bonds="4" />
<Atom name="CE" tinkerLookupName="CE" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD" bonds="1" />
<Atom name="HD3" tinkerLookupName="HD" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE" bonds="1" />
<Atom name="HE3" tinkerLookupName="HE" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="HZ1" tinkerLookupName="HZ" bonds="1" />
<Atom name="HZ2" tinkerLookupName="HZ" bonds="1" />
<Atom name="HZ3" tinkerLookupName="HZ" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="NZ" tinkerLookupName="NZ" bonds="4" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD" to="HD3" />
<Bond from="CD" to="CG" />
<Bond from="CD" to="HD2" />
<Bond from="CD" to="CE" />
<Bond from="CE" to="NZ" />
<Bond from="CE" to="HE2" />
<Bond from="CE" to="HE3" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
<Bond from="H" to="N" />
<Bond from="HZ1" to="NZ" />
<Bond from="HZ2" to="NZ" />
<Bond from="HZ3" to="NZ" />
</Residue>
<Residue abbreviation="LYD" loc="middle" type="protein" tinkerLookupName="Lysine (NH2)" fullName="Lysine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD" tinkerLookupName="CD" bonds="4" />
<Atom name="CE" tinkerLookupName="CE" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD" bonds="1" />
<Atom name="HD3" tinkerLookupName="HD" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE" bonds="1" />
<Atom name="HE3" tinkerLookupName="HE" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="HZ1" tinkerLookupName="HZ" bonds="1" />
<Atom name="HZ2" tinkerLookupName="HZ" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="NZ" tinkerLookupName="NZ" bonds="4" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD" to="HD3" />
<Bond from="CD" to="CG" />
<Bond from="CD" to="HD2" />
<Bond from="CD" to="CE" />
<Bond from="CE" to="NZ" />
<Bond from="CE" to="HE2" />
<Bond from="CE" to="HE3" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
<Bond from="H" to="N" />
<Bond from="HZ1" to="NZ" />
<Bond from="HZ2" to="NZ" />
</Residue>
<Residue abbreviation="MET" loc="middle" type="protein" tinkerLookupName="Methionine" fullName="Methionine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CE" tinkerLookupName="CE" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE" bonds="1" />
<Atom name="HE3" tinkerLookupName="HE" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="SD" tinkerLookupName="SD" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CE" to="SD" />
<Bond from="CE" to="HE1" />
<Bond from="CE" to="HE2" />
<Bond from="CE" to="HE3" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
<Bond from="CG" to="SD" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="PHE" loc="middle" type="protein" tinkerLookupName="Phenylalanine" fullName="Phenylalanine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD1" tinkerLookupName="CD" bonds="3" />
<Atom name="CD2" tinkerLookupName="CD" bonds="3" />
<Atom name="CE1" tinkerLookupName="CE" bonds="3" />
<Atom name="CE2" tinkerLookupName="CE" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="CZ" tinkerLookupName="CZ" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD1" tinkerLookupName="HD" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE" bonds="1" />
<Atom name="HZ" tinkerLookupName="HZ" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD1" to="CG" />
<Bond from="CD1" to="CE1" />
<Bond from="CD1" to="HD1" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="CE2" />
<Bond from="CD2" to="HD2" />
<Bond from="CE1" to="CZ" />
<Bond from="CE1" to="HE1" />
<Bond from="CE2" to="CZ" />
<Bond from="CE2" to="HE2" />
<Bond from="CZ" to="HZ" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="PRO" loc="middle" type="protein" tinkerLookupName="Proline" fullName="Proline">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD" tinkerLookupName="CD" bonds="4" />
<Atom name="CG" tinkerLookupName="CG" bonds="4" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD" bonds="1" />
<Atom name="HD3" tinkerLookupName="HD" bonds="1" />
<Atom name="HG2" tinkerLookupName="HG" bonds="1" />
<Atom name="HG3" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="4" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD" to="CG" />
<Bond from="CD" to="HD3" />
<Bond from="CD" to="HD2" />
<Bond from="CD" to="N" />
<Bond from="CG" to="HG2" />
<Bond from="CG" to="HG3" />
</Residue>
<Residue abbreviation="SER" loc="middle" type="protein" tinkerLookupName="Serine" fullName="Serine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HG" tinkerLookupName="HG" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OG" tinkerLookupName="OG" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="OG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="H" to="N" />
<Bond from="HG" to="OG" />
</Residue>
<Residue abbreviation="THR" loc="middle" type="protein" tinkerLookupName="Threonine" fullName="Threonine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CG2" tinkerLookupName="CG2" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB" tinkerLookupName="HB" bonds="1" />
<Atom name="HG1" tinkerLookupName="HG1" bonds="1" />
<Atom name="HG21" tinkerLookupName="HG2" bonds="1" />
<Atom name="HG22" tinkerLookupName="HG2" bonds="1" />
<Atom name="HG23" tinkerLookupName="HG2" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OG1" tinkerLookupName="OG1" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="HB" />
<Bond from="CB" to="CG2" />
<Bond from="CB" to="OG1" />
<Bond from="CG2" to="HG21" />
<Bond from="CG2" to="HG23" />
<Bond from="CG2" to="HG22" />
<Bond from="H" to="N" />
<Bond from="HG1" to="OG1" />
</Residue>
<Residue abbreviation="TRP" loc="middle" type="protein" tinkerLookupName="Tryptophan" fullName="Tryptophan">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD1" tinkerLookupName="CD1" bonds="3" />
<Atom name="CD2" tinkerLookupName="CD2" bonds="3" />
<Atom name="CE2" tinkerLookupName="CE2" bonds="3" />
<Atom name="CE3" tinkerLookupName="CE3" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="CH2" tinkerLookupName="CH2" bonds="3" />
<Atom name="CZ2" tinkerLookupName="CZ2" bonds="3" />
<Atom name="CZ3" tinkerLookupName="CZ3" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD1" tinkerLookupName="HD1" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE1" bonds="1" />
<Atom name="HE3" tinkerLookupName="HE3" bonds="1" />
<Atom name="HH2" tinkerLookupName="HH2" bonds="1" />
<Atom name="HZ2" tinkerLookupName="HZ2" bonds="1" />
<Atom name="HZ3" tinkerLookupName="HZ3" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="NE1" tinkerLookupName="NE1" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD1" to="CG" />
<Bond from="CD1" to="HD1" />
<Bond from="CD1" to="NE1" />
<Bond from="CD2" to="CE3" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="CE2" />
<Bond from="CE2" to="CZ2" />
<Bond from="CE2" to="NE1" />
<Bond from="CE3" to="CZ3" />
<Bond from="CE3" to="HE3" />
<Bond from="CH2" to="CZ2" />
<Bond from="CH2" to="HH2" />
<Bond from="CH2" to="CZ3" />
<Bond from="CZ2" to="HZ2" />
<Bond from="CZ3" to="HZ3" />
<Bond from="H" to="N" />
<Bond from="HE1" to="NE1" />
</Residue>
<Residue abbreviation="TYR" loc="middle" type="protein" tinkerLookupName="Tyrosine" fullName="Tyrosine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD1" tinkerLookupName="CD" bonds="3" />
<Atom name="CD2" tinkerLookupName="CD" bonds="3" />
<Atom name="CE1" tinkerLookupName="CE" bonds="3" />
<Atom name="CE2" tinkerLookupName="CE" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="CZ" tinkerLookupName="CZ" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD1" tinkerLookupName="HD" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE" bonds="1" />
<Atom name="HH" tinkerLookupName="HH" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OH" tinkerLookupName="OH" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD1" to="CG" />
<Bond from="CD1" to="CE1" />
<Bond from="CD1" to="HD1" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="CE2" />
<Bond from="CD2" to="HD2" />
<Bond from="CE1" to="CZ" />
<Bond from="CE1" to="HE1" />
<Bond from="CE2" to="CZ" />
<Bond from="CE2" to="HE2" />
<Bond from="CZ" to="OH" />
<Bond from="H" to="N" />
<Bond from="HH" to="OH" />
</Residue>
<Residue abbreviation="TYD" loc="middle" type="protein" tinkerLookupName="Tyrosine (O-)" fullName="Tyrosine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CD1" tinkerLookupName="CD" bonds="3" />
<Atom name="CD2" tinkerLookupName="CD" bonds="3" />
<Atom name="CE1" tinkerLookupName="CE" bonds="3" />
<Atom name="CE2" tinkerLookupName="CE" bonds="3" />
<Atom name="CG" tinkerLookupName="CG" bonds="3" />
<Atom name="CZ" tinkerLookupName="CZ" bonds="3" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB2" tinkerLookupName="HB" bonds="1" />
<Atom name="HB3" tinkerLookupName="HB" bonds="1" />
<Atom name="HD1" tinkerLookupName="HD" bonds="1" />
<Atom name="HD2" tinkerLookupName="HD" bonds="1" />
<Atom name="HE1" tinkerLookupName="HE" bonds="1" />
<Atom name="HE2" tinkerLookupName="HE" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Atom name="OH" tinkerLookupName="OH" bonds="2" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG" />
<Bond from="CB" to="HB3" />
<Bond from="CB" to="HB2" />
<Bond from="CD1" to="CG" />
<Bond from="CD1" to="CE1" />
<Bond from="CD1" to="HD1" />
<Bond from="CD2" to="CG" />
<Bond from="CD2" to="CE2" />
<Bond from="CD2" to="HD2" />
<Bond from="CE1" to="CZ" />
<Bond from="CE1" to="HE1" />
<Bond from="CE2" to="CZ" />
<Bond from="CE2" to="HE2" />
<Bond from="CZ" to="OH" />
<Bond from="H" to="N" />
</Residue>
<Residue abbreviation="VAL" loc="middle" type="protein" tinkerLookupName="Valine" fullName="Valine">
<Atom name="C" tinkerLookupName="C" bonds="3" />
<Atom name="CA" tinkerLookupName="CA" bonds="4" />
<Atom name="CB" tinkerLookupName="CB" bonds="4" />
<Atom name="CG1" tinkerLookupName="CG1" bonds="4" />
<Atom name="CG2" tinkerLookupName="CG2" bonds="4" />
<Atom name="H" tinkerLookupName="HN" bonds="1" />
<Atom name="HA" tinkerLookupName="HA" bonds="1" />
<Atom name="HB" tinkerLookupName="HB" bonds="1" />
<Atom name="HG11" tinkerLookupName="HG1" bonds="1" />
<Atom name="HG12" tinkerLookupName="HG1" bonds="1" />
<Atom name="HG13" tinkerLookupName="HG1" bonds="1" />
<Atom name="HG21" tinkerLookupName="HG2" bonds="1" />
<Atom name="HG22" tinkerLookupName="HG2" bonds="1" />
<Atom name="HG23" tinkerLookupName="HG2" bonds="1" />
<Atom name="N" tinkerLookupName="N" bonds="3" />
<Atom name="O" tinkerLookupName="O" bonds="1" />
<Bond from="C" to="CA" />
<Bond from="C" to="O" />
<Bond from="CA" to="CB" />
<Bond from="CA" to="HA" />
<Bond from="CA" to="N" />
<Bond from="CB" to="CG1" />
<Bond from="CB" to="HB" />
<Bond from="CB" to="CG2" />
<Bond from="CG1" to="HG11" />
<Bond from="CG1" to="HG12" />
<Bond from="CG1" to="HG13" />
<Bond from="CG2" to="HG21" />
<Bond from="CG2" to="HG23" />
<Bond from="CG2" to="HG22" />
<Bond from="H" to="N" />
</Residue>
</Residues>
wrappers/python/simtk/openmm/app/data/amoeba2013.xml
View file @ 245a7380
<ForceField>
<Info>
<Source>amoebapro13_5-2014.prm</Source>
<DateGenerated>2014-05-08</DateGenerated>
<Source>amoebapro13.prm</Source>
<DateGenerated>2015-02-19</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>
</Info>
<AtomTypes>
......@@ -170,7 +170,7 @@
<Type name="163" class="32" element="C" mass="12.011"/>
<Type name="164" class="33" element="O" mass="15.999"/>
<Type name="165" class="34" element="O" mass="15.999"/>
<Type name="166" class="35" element="H" mass="15.999"/>
<Type name="166" class="35" element="H" mass="1.008"/>
<Type name="167" class="8" element="C" mass="12.011"/>
<Type name="168" class="9" element="H" mass="1.008"/>
<Type name="169" class="8" element="C" mass="12.011"/>
......
wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml
View file @ 245a7380
<ForceField>
<Info>
<Source>amoebapro13_5-2014.prm</Source>
<DateGenerated>2014-05-08</DateGenerated>
<Source>amoebapro13.prm</Source>
<DateGenerated>2015-02-19</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>
</Info>
<AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">
......
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