Pocket-Gen / pdbfixer /soft.xml
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<ForceField>
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<Bond from="1" to="2"/>
<Bond from="1" to="10"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="9"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="6" to="8"/>
<Bond from="8" to="9"/>
<Bond from="10" to="11"/>
<ExternalBond from="0"/>
<ExternalBond from="10"/>
</Residue>
<Residue name="NTHR">
<Atom name="N" type="963"/>
<Atom name="CA" type="965"/>
<Atom name="CB" type="967"/>
<Atom name="CG2" type="969"/>
<Atom name="OG1" type="971"/>
<Atom name="C" type="973"/>
<Atom name="O" type="974"/>
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<Bond from="1" to="2"/>
<Bond from="1" to="5"/>
<Bond from="2" to="3"/>
<Bond from="2" to="4"/>
<Bond from="5" to="6"/>
<ExternalBond from="5"/>
</Residue>
<Residue name="DTN">
<Atom name="O5'" type="1452"/>
<Atom name="C5'" type="1453"/>
<Atom name="C4'" type="1455"/>
<Atom name="O4'" type="1457"/>
<Atom name="C1'" type="1458"/>
<Atom name="N1" type="1460"/>
<Atom name="C6" type="1461"/>
<Atom name="C5" type="1463"/>
<Atom name="C7" type="1464"/>
<Atom name="C4" type="1466"/>
<Atom name="O4" type="1467"/>
<Atom name="N3" type="1468"/>
<Atom name="C2" type="1470"/>
<Atom name="O2" type="1471"/>
<Atom name="C3'" type="1472"/>
<Atom name="C2'" type="1474"/>
<Atom name="O3'" type="1476"/>
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<Bond from="1" to="2"/>
<Bond from="2" to="3"/>
<Bond from="2" to="14"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="4" to="15"/>
<Bond from="5" to="6"/>
<Bond from="5" to="12"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="7" to="9"/>
<Bond from="9" to="10"/>
<Bond from="9" to="11"/>
<Bond from="11" to="12"/>
<Bond from="12" to="13"/>
<Bond from="14" to="15"/>
<Bond from="14" to="16"/>
</Residue>
<Residue name="CPHE">
<Atom name="N" type="590"/>
<Atom name="CA" type="592"/>
<Atom name="CB" type="594"/>
<Atom name="CG" type="596"/>
<Atom name="CD1" type="597"/>
<Atom name="CE1" type="599"/>
<Atom name="CZ" type="601"/>
<Atom name="CE2" type="603"/>
<Atom name="CD2" type="605"/>
<Atom name="C" type="607"/>
<Atom name="O" type="608"/>
<Atom name="OXT" type="609"/>
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<Bond from="1" to="9"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="8"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="9" to="10"/>
<Bond from="9" to="11"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="NHIS">
<Atom name="N" type="816"/>
<Atom name="CA" type="818"/>
<Atom name="CB" type="820"/>
<Atom name="CG" type="822"/>
<Atom name="ND1" type="823"/>
<Atom name="CE1" type="825"/>
<Atom name="NE2" type="827"/>
<Atom name="CD2" type="828"/>
<Atom name="C" type="830"/>
<Atom name="O" type="831"/>
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<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="MG2">
<Atom name="MG" type="1958"/>
</Residue>
<Residue name="NHE">
<Atom name="N" type="704"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="NLYS">
<Atom name="N" type="893"/>
<Atom name="CA" type="895"/>
<Atom name="CB" type="897"/>
<Atom name="CG" type="899"/>
<Atom name="CD" type="901"/>
<Atom name="CE" type="903"/>
<Atom name="NZ" type="905"/>
<Atom name="C" type="907"/>
<Atom name="O" type="908"/>
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<Bond from="1" to="2"/>
<Bond from="1" to="7"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="7" to="8"/>
<ExternalBond from="7"/>
</Residue>
<Residue name="RGN">
<Atom name="O5'" type="1810"/>
<Atom name="C5'" type="1811"/>
<Atom name="C4'" type="1813"/>
<Atom name="O4'" type="1815"/>
<Atom name="C1'" type="1816"/>
<Atom name="N9" type="1818"/>
<Atom name="C8" type="1819"/>
<Atom name="N7" type="1821"/>
<Atom name="C5" type="1822"/>
<Atom name="C6" type="1823"/>
<Atom name="O6" type="1824"/>
<Atom name="N1" type="1825"/>
<Atom name="C2" type="1827"/>
<Atom name="N2" type="1828"/>
<Atom name="N3" type="1830"/>
<Atom name="C4" type="1831"/>
<Atom name="C3'" type="1832"/>
<Atom name="C2'" type="1834"/>
<Atom name="O2'" type="1836"/>
<Atom name="O3'" type="1838"/>
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<Bond from="1" to="2"/>
<Bond from="2" to="3"/>
<Bond from="2" to="16"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="4" to="17"/>
<Bond from="5" to="6"/>
<Bond from="5" to="15"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="8" to="9"/>
<Bond from="8" to="15"/>
<Bond from="9" to="10"/>
<Bond from="9" to="11"/>
<Bond from="11" to="12"/>
<Bond from="12" to="13"/>
<Bond from="12" to="14"/>
<Bond from="14" to="15"/>
<Bond from="16" to="17"/>
<Bond from="16" to="19"/>
<Bond from="17" to="18"/>
</Residue>
<Residue name="CGLU">
<Atom name="N" type="456"/>
<Atom name="CA" type="458"/>
<Atom name="CB" type="460"/>
<Atom name="CG" type="462"/>
<Atom name="CD" type="464"/>
<Atom name="OE1" type="465"/>
<Atom name="OE2" type="466"/>
<Atom name="C" type="467"/>
<Atom name="O" type="468"/>
<Atom name="OXT" type="469"/>
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<Bond from="1" to="2"/>
<Bond from="1" to="7"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="4" to="6"/>
<Bond from="7" to="8"/>
<Bond from="7" to="9"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="CGLY">
<Atom name="N" type="470"/>
<Atom name="CA" type="472"/>
<Atom name="C" type="474"/>
<Atom name="O" type="475"/>
<Atom name="OXT" type="476"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="2" to="3"/>
<Bond from="2" to="4"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="CGLN">
<Atom name="N" type="441"/>
<Atom name="CA" type="443"/>
<Atom name="CB" type="445"/>
<Atom name="CG" type="447"/>
<Atom name="CD" type="449"/>
<Atom name="OE1" type="450"/>
<Atom name="NE2" type="451"/>
<Atom name="C" type="453"/>
<Atom name="O" type="454"/>
<Atom name="OXT" type="455"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="7"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="4" to="6"/>
<Bond from="7" to="8"/>
<Bond from="7" to="9"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="NARG">
<Atom name="N" type="722"/>
<Atom name="CA" type="724"/>
<Atom name="CB" type="726"/>
<Atom name="CG" type="728"/>
<Atom name="CD" type="730"/>
<Atom name="NE" type="732"/>
<Atom name="CZ" type="734"/>
<Atom name="NH1" type="735"/>
<Atom name="NH2" type="737"/>
<Atom name="C" type="739"/>
<Atom name="O" type="740"/>
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<Bond from="1" to="2"/>
<Bond from="1" to="9"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="6" to="8"/>
<Bond from="9" to="10"/>
<ExternalBond from="9"/>
</Residue>
<Residue name="RU5">
<Atom name="O5'" type="1900"/>
<Atom name="C5'" type="1901"/>
<Atom name="C4'" type="1903"/>
<Atom name="O4'" type="1905"/>
<Atom name="C1'" type="1906"/>
<Atom name="N1" type="1908"/>
<Atom name="C6" type="1909"/>
<Atom name="C5" type="1911"/>
<Atom name="C4" type="1913"/>
<Atom name="O4" type="1914"/>
<Atom name="N3" type="1915"/>
<Atom name="C2" type="1917"/>
<Atom name="O2" type="1918"/>
<Atom name="C3'" type="1919"/>
<Atom name="C2'" type="1921"/>
<Atom name="O2'" type="1923"/>
<Atom name="O3'" type="1925"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="2" to="3"/>
<Bond from="2" to="13"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="4" to="14"/>
<Bond from="5" to="6"/>
<Bond from="5" to="11"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="8" to="9"/>
<Bond from="8" to="10"/>
<Bond from="10" to="11"/>
<Bond from="11" to="12"/>
<Bond from="13" to="14"/>
<Bond from="13" to="16"/>
<Bond from="14" to="15"/>
<ExternalBond from="16"/>
</Residue>
<Residue name="NTYR">
<Atom name="N" type="998"/>
<Atom name="CA" type="1000"/>
<Atom name="CB" type="1002"/>
<Atom name="CG" type="1004"/>
<Atom name="CD1" type="1005"/>
<Atom name="CE1" type="1007"/>
<Atom name="CZ" type="1009"/>
<Atom name="OH" type="1010"/>
<Atom name="CE2" type="1012"/>
<Atom name="CD2" type="1014"/>
<Atom name="C" type="1016"/>
<Atom name="O" type="1017"/>
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<Bond from="1" to="2"/>
<Bond from="1" to="10"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="9"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="6" to="8"/>
<Bond from="8" to="9"/>
<Bond from="10" to="11"/>
<ExternalBond from="10"/>
</Residue>
<Residue name="CPRO">
<Atom name="N" type="610"/>
<Atom name="CD" type="611"/>
<Atom name="CG" type="613"/>
<Atom name="CB" type="615"/>
<Atom name="CA" type="617"/>
<Atom name="C" type="619"/>
<Atom name="O" type="620"/>
<Atom name="OXT" type="621"/>
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<Bond from="0" to="4"/>
<Bond from="1" to="2"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="5" to="7"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="Cs+">
<Atom name="Cs+" type="1955"/>
</Residue>
<Residue name="TRP">
<Atom name="N" type="311"/>
<Atom name="CA" type="313"/>
<Atom name="CB" type="315"/>
<Atom name="CG" type="317"/>
<Atom name="CD1" type="318"/>
<Atom name="NE1" type="320"/>
<Atom name="CE2" type="322"/>
<Atom name="CZ2" type="323"/>
<Atom name="CH2" type="325"/>
<Atom name="CZ3" type="327"/>
<Atom name="CE3" type="329"/>
<Atom name="CD2" type="331"/>
<Atom name="C" type="332"/>
<Atom name="O" type="333"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="12"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="11"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="6" to="11"/>
<Bond from="7" to="8"/>
<Bond from="8" to="9"/>
<Bond from="9" to="10"/>
<Bond from="10" to="11"/>
<Bond from="12" to="13"/>
<ExternalBond from="0"/>
<ExternalBond from="12"/>
</Residue>
<Residue name="NSER">
<Atom name="N" type="953"/>
<Atom name="CA" type="955"/>
<Atom name="CB" type="957"/>
<Atom name="OG" type="959"/>
<Atom name="C" type="961"/>
<Atom name="O" type="962"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="4"/>
<Bond from="2" to="3"/>
<Bond from="4" to="5"/>
<ExternalBond from="4"/>
</Residue>
<Residue name="NASP">
<Atom name="N" type="753"/>
<Atom name="CA" type="755"/>
<Atom name="CB" type="757"/>
<Atom name="CG" type="759"/>
<Atom name="OD1" type="760"/>
<Atom name="OD2" type="761"/>
<Atom name="C" type="762"/>
<Atom name="O" type="763"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="6"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="5"/>
<Bond from="6" to="7"/>
<ExternalBond from="6"/>
</Residue>
<Residue name="RG3">
<Atom name="P" type="1746"/>
<Atom name="O1P" type="1747"/>
<Atom name="O2P" type="1748"/>
<Atom name="O5'" type="1749"/>
<Atom name="C5'" type="1750"/>
<Atom name="C4'" type="1752"/>
<Atom name="O4'" type="1754"/>
<Atom name="C1'" type="1755"/>
<Atom name="N9" type="1757"/>
<Atom name="C8" type="1758"/>
<Atom name="N7" type="1760"/>
<Atom name="C5" type="1761"/>
<Atom name="C6" type="1762"/>
<Atom name="O6" type="1763"/>
<Atom name="N1" type="1764"/>
<Atom name="C2" type="1766"/>
<Atom name="N2" type="1767"/>
<Atom name="N3" type="1769"/>
<Atom name="C4" type="1770"/>
<Atom name="C3'" type="1771"/>
<Atom name="C2'" type="1773"/>
<Atom name="O2'" type="1775"/>
<Atom name="O3'" type="1777"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<Bond from="0" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="5" to="19"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="7" to="20"/>
<Bond from="8" to="9"/>
<Bond from="8" to="18"/>
<Bond from="9" to="10"/>
<Bond from="10" to="11"/>
<Bond from="11" to="12"/>
<Bond from="11" to="18"/>
<Bond from="12" to="13"/>
<Bond from="12" to="14"/>
<Bond from="14" to="15"/>
<Bond from="15" to="16"/>
<Bond from="15" to="17"/>
<Bond from="17" to="18"/>
<Bond from="19" to="20"/>
<Bond from="19" to="22"/>
<Bond from="20" to="21"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="RG5">
<Atom name="O5'" type="1780"/>
<Atom name="C5'" type="1781"/>
<Atom name="C4'" type="1783"/>
<Atom name="O4'" type="1785"/>
<Atom name="C1'" type="1786"/>
<Atom name="N9" type="1788"/>
<Atom name="C8" type="1789"/>
<Atom name="N7" type="1791"/>
<Atom name="C5" type="1792"/>
<Atom name="C6" type="1793"/>
<Atom name="O6" type="1794"/>
<Atom name="N1" type="1795"/>
<Atom name="C2" type="1797"/>
<Atom name="N2" type="1798"/>
<Atom name="N3" type="1800"/>
<Atom name="C4" type="1801"/>
<Atom name="C3'" type="1802"/>
<Atom name="C2'" type="1804"/>
<Atom name="O2'" type="1806"/>
<Atom name="O3'" type="1808"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="2" to="3"/>
<Bond from="2" to="16"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="4" to="17"/>
<Bond from="5" to="6"/>
<Bond from="5" to="15"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="8" to="9"/>
<Bond from="8" to="15"/>
<Bond from="9" to="10"/>
<Bond from="9" to="11"/>
<Bond from="11" to="12"/>
<Bond from="12" to="13"/>
<Bond from="12" to="14"/>
<Bond from="14" to="15"/>
<Bond from="16" to="17"/>
<Bond from="16" to="19"/>
<Bond from="17" to="18"/>
<ExternalBond from="19"/>
</Residue>
<Residue name="NPHE">
<Atom name="N" type="922"/>
<Atom name="CA" type="924"/>
<Atom name="CB" type="926"/>
<Atom name="CG" type="928"/>
<Atom name="CD1" type="929"/>
<Atom name="CE1" type="931"/>
<Atom name="CZ" type="933"/>
<Atom name="CE2" type="935"/>
<Atom name="CD2" type="937"/>
<Atom name="C" type="939"/>
<Atom name="O" type="940"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="9"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="8"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="9" to="10"/>
<ExternalBond from="9"/>
</Residue>
<Residue name="DT3">
<Atom name="P" type="1396"/>
<Atom name="O1P" type="1397"/>
<Atom name="O2P" type="1398"/>
<Atom name="O5'" type="1399"/>
<Atom name="C5'" type="1400"/>
<Atom name="C4'" type="1402"/>
<Atom name="O4'" type="1404"/>
<Atom name="C1'" type="1405"/>
<Atom name="N1" type="1407"/>
<Atom name="C6" type="1408"/>
<Atom name="C5" type="1410"/>
<Atom name="C7" type="1411"/>
<Atom name="C4" type="1413"/>
<Atom name="O4" type="1414"/>
<Atom name="N3" type="1415"/>
<Atom name="C2" type="1417"/>
<Atom name="O2" type="1418"/>
<Atom name="C3'" type="1419"/>
<Atom name="C2'" type="1421"/>
<Atom name="O3'" type="1423"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<Bond from="0" to="3"/>
<Bond from="3" to="4"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="5" to="17"/>
<Bond from="6" to="7"/>
<Bond from="7" to="8"/>
<Bond from="7" to="18"/>
<Bond from="8" to="9"/>
<Bond from="8" to="15"/>
<Bond from="9" to="10"/>
<Bond from="10" to="11"/>
<Bond from="10" to="12"/>
<Bond from="12" to="13"/>
<Bond from="12" to="14"/>
<Bond from="14" to="15"/>
<Bond from="15" to="16"/>
<Bond from="17" to="18"/>
<Bond from="17" to="19"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="NASN">
<Atom name="N" type="741"/>
<Atom name="CA" type="743"/>
<Atom name="CB" type="745"/>
<Atom name="CG" type="747"/>
<Atom name="OD1" type="748"/>
<Atom name="ND2" type="749"/>
<Atom name="C" type="751"/>
<Atom name="O" type="752"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="6"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="5"/>
<Bond from="6" to="7"/>
<ExternalBond from="6"/>
</Residue>
<Residue name="DT5">
<Atom name="O5'" type="1426"/>
<Atom name="C5'" type="1427"/>
<Atom name="C4'" type="1429"/>
<Atom name="O4'" type="1431"/>
<Atom name="C1'" type="1432"/>
<Atom name="N1" type="1434"/>
<Atom name="C6" type="1435"/>
<Atom name="C5" type="1437"/>
<Atom name="C7" type="1438"/>
<Atom name="C4" type="1440"/>
<Atom name="O4" type="1441"/>
<Atom name="N3" type="1442"/>
<Atom name="C2" type="1444"/>
<Atom name="O2" type="1445"/>
<Atom name="C3'" type="1446"/>
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<Proper class1="C" class2="CV" class3="NB" class4="C" periodicity1="2" phase1="3.14159" k1="10.0416" />
<Proper class1="C" class2="CR" class3="NB" class4="C" periodicity1="2" phase1="3.14159" k1="20.92" />
<Proper class1="C" class2="CR" class3="NA" class4="C" periodicity1="2" phase1="3.14159" k1="9.7278" />
<Proper class1="C" class2="C*" class3="CW" class4="C" periodicity1="2" phase1="3.14159" k1="27.3006" />
<Proper class1="C" class2="C*" class3="CT" class4="C" periodicity1="2" phase1="0" k1="0" />
<Proper class1="C" class2="C*" class3="CB" class4="C" periodicity1="2" phase1="3.14159" k1="7.0082" />
<Proper class1="C" class2="CT" class3="SH" class4="C" periodicity1="3" phase1="0" k1="1.046" />
<Proper class1="C" class2="CT" class3="S" class4="C" periodicity1="3" phase1="0" k1="1.39467" />
<Proper class1="C" class2="CT" class3="OS" class4="C" periodicity1="3" phase1="0" k1="1.60387" />
<Proper class1="C" class2="CT" class3="OH" class4="C" periodicity1="3" phase1="0" k1="0.697333" />
<Proper class1="C" class2="CT" class3="N3" class4="C" periodicity1="3" phase1="0" k1="0.650844" />
<Proper class1="C" class2="CT" class3="N2" class4="C" periodicity1="3" phase1="0" k1="0" />
<Proper class1="C" class2="CT" class3="N*" class4="C" periodicity1="2" phase1="0" k1="0" />
<Proper class1="C" class2="CT" class3="N" class4="C" periodicity1="2" phase1="0" k1="0" />
<Proper class1="C" class2="CT" class3="CT" class4="C" periodicity1="3" phase1="0" k1="0.650844" />
<Proper class1="C" class2="CQ" class3="NC" class4="C" periodicity1="2" phase1="3.14159" k1="28.4512" />
<Proper class1="C" class2="CN" class3="NA" class4="C" periodicity1="2" phase1="3.14159" k1="6.3806" />
<Proper class1="C" class2="CM" class3="OS" class4="C" periodicity1="2" phase1="3.14159" k1="4.3932" />
<Proper class1="C" class2="CM" class3="N*" class4="C" periodicity1="2" phase1="3.14159" k1="7.7404" />
<Proper class1="C" class2="CM" class3="CT" class4="C" periodicity1="3" phase1="0" k1="0" />
<Proper class1="C" class2="CM" class3="CM" class4="C" periodicity1="2" phase1="3.14159" k1="27.8236" />
<Proper class1="C" class2="CK" class3="NB" class4="C" periodicity1="2" phase1="3.14159" k1="41.84" />
<Proper class1="C" class2="CK" class3="N*" class4="C" periodicity1="2" phase1="3.14159" k1="7.1128" />
<Proper class1="C" class2="CC" class3="NB" class4="C" periodicity1="2" phase1="3.14159" k1="10.0416" />
<Proper class1="C" class2="CC" class3="NA" class4="C" periodicity1="2" phase1="3.14159" k1="5.8576" />
<Proper class1="C" class2="CC" class3="CW" class4="C" periodicity1="2" phase1="3.14159" k1="22.489" />
<Proper class1="C" class2="CC" class3="CV" class4="C" periodicity1="2" phase1="3.14159" k1="21.5476" />
<Proper class1="C" class2="CC" class3="CT" class4="C" periodicity1="2" phase1="0" k1="0" />
<Proper class1="C" class2="CB" class3="NC" class4="C" periodicity1="2" phase1="3.14159" k1="17.3636" />
<Proper class1="C" class2="CB" class3="NB" class4="C" periodicity1="2" phase1="3.14159" k1="10.6692" />
<Proper class1="C" class2="CB" class3="N*" class4="C" periodicity1="2" phase1="3.14159" k1="6.9036" />
<Proper class1="C" class2="CB" class3="CN" class4="C" periodicity1="2" phase1="3.14159" k1="12.552" />
<Proper class1="C" class2="CB" class3="CB" class4="C" periodicity1="2" phase1="3.14159" k1="22.8028" />
<Proper class1="C" class2="CA" class3="OH" class4="C" periodicity1="2" phase1="3.14159" k1="3.7656" />
<Proper class1="C" class2="CA" class3="NC" class4="C" periodicity1="2" phase1="3.14159" k1="20.0832" />
<Proper class1="C" class2="CA" class3="NA" class4="C" periodicity1="2" phase1="3.14159" k1="6.276" />
<Proper class1="C" class2="CA" class3="N2" class4="C" periodicity1="2" phase1="3.14159" k1="10.0416" />
<Proper class1="C" class2="CA" class3="CT" class4="C" periodicity1="2" phase1="0" k1="0" />
<Proper class1="C" class2="CA" class3="CN" class4="C" periodicity1="2" phase1="3.14159" k1="15.167" />
<Proper class1="C" class2="CA" class3="CM" class4="C" periodicity1="2" phase1="3.14159" k1="10.6692" />
<Proper class1="C" class2="CA" class3="CB" class4="C" periodicity1="2" phase1="3.14159" k1="14.644" />
<Proper class1="C" class2="CA" class3="CA" class4="C" periodicity1="2" phase1="3.14159" k1="15.167" />
<Proper class1="C" class2="C" class3="OS" class4="C" periodicity1="2" phase1="3.14159" k1="11.2968" />
<Proper class1="C" class2="C" class3="OH" class4="C" periodicity1="2" phase1="3.14159" k1="9.6232" />
<Proper class1="C" class2="C" class3="O" class4="C" periodicity1="2" phase1="3.14159" k1="11.7152" />
<Proper class1="C" class2="C" class3="NC" class4="C" periodicity1="2" phase1="3.14159" k1="16.736" />
<Proper class1="C" class2="C" class3="NA" class4="C" periodicity1="2" phase1="3.14159" k1="5.6484" />
<Proper class1="C" class2="C" class3="N*" class4="C" periodicity1="2" phase1="3.14159" k1="6.0668" />
<Proper class1="C" class2="C" class3="N" class4="C" periodicity1="2" phase1="3.14159" k1="10.46" />
<Proper class1="C" class2="C" class3="CM" class4="C" periodicity1="2" phase1="3.14159" k1="9.1002" />
<Proper class1="C" class2="C" class3="CB" class4="C" periodicity1="2" phase1="3.14159" k1="12.552" />
<Proper class1="C" class2="C" class3="CA" class4="C" periodicity1="2" phase1="3.14159" k1="15.167" />
<Proper class1="C" class2="C" class3="C" class4="C" periodicity1="2" phase1="3.14159" k1="15.167" />
<Improper class1="C5" class2="C" class3="C" class4="O" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C6" class2="C" class3="O2" class4="O2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="N" class2="C5" class3="CT" class4="O" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="N" class2="C" class3="CT" class4="O" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CA" class2="CA" class3="CA" class4="OH" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="C" class2="CA" class3="CA" class4="OH" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CA" class2="N2" class3="NA" class4="NC" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CA" class2="CB" class3="N2" class4="NC" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CA" class2="CM" class3="N2" class4="NC" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CM" class2="C" class3="CM" class4="CT" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CA" class2="CA" class3="CA" class4="CT" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="C*" class2="CB" class3="CT" class4="CW" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CC" class2="CT" class3="CW" class4="NA" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CC" class2="CT" class3="CW" class4="NB" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CC" class2="CT" class3="CV" class4="NA" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="C" class2="CT" class3="O" class4="OH" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="N*" class2="C" class3="CM" class4="CT" periodicity1="2" phase1="3.14159" k1="4.184" />
<Improper class1="N*" class2="CB" class3="CK" class4="CT" periodicity1="2" phase1="3.14159" k1="4.184" />
<Improper class1="N" class2="C" class3="CT" class4="CT" periodicity1="2" phase1="3.14159" k1="4.184" />
<Improper class1="CA" class2="C" class3="N2" class4="N2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C" class2="C" class3="O2" class4="O2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C" class2="C" class3="C" class4="O" periodicity1="2" phase1="3.14159" k1="43.932" />
</PeriodicTorsionForce>
<Script>
import openmm as mm
nb = mm.CustomNonbondedForce('C/((r/0.2)^4+1)')
nb.addGlobalParameter('C', 1.0)
sys.addForce(nb)
for i in range(sys.getNumParticles()):
nb.addParticle([])
exclusions = set()
for bond in data.bonds:
exclusions.add((min(bond.atom1, bond.atom2), max(bond.atom1, bond.atom2)))
for angle in data.angles:
exclusions.add((min(angle[0], angle[2]), max(angle[0], angle[2])))
for a1, a2 in exclusions:
nb.addExclusion(a1, a2)
</Script>
</ForceField>