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Commit aa4dad89 authored by Peter Eastman's avatar Peter Eastman
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Changes to read more PDB files with nucleic acids correctly

parent f472d424
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Showing with 22 additions and 13 deletions
wrappers/python/simtk/openmm/app/data/pdbNames.xml
View file @ aa4dad89
...@@ -25,14 +25,15 @@ ...@@ -25,14 +25,15 @@
<Atom name="O4'" alt1="O4*"/> <Atom name="O4'" alt1="O4*"/>
<Atom name="O5'" alt1="O5*"/> <Atom name="O5'" alt1="O5*"/>
<Atom name="H1'" alt1="H1*"/> <Atom name="H1'" alt1="H1*"/>
<Atom name="H2'" alt1="H2*" alt2="1H2*"/> <Atom name="H2'" alt1="H2*" alt2="1H2*" alt3="1H2'"/>
<Atom name="H2''" alt1="2H2*"/> <Atom name="H2''" alt1="2H2*" alt2="2H2'"/>
<Atom name="H3'" alt1="H3*"/> <Atom name="H3'" alt1="H3*"/>
<Atom name="H4'" alt1="H4*"/> <Atom name="H4'" alt1="H4*"/>
<Atom name="H5'" alt1="1H5*"/> <Atom name="H5'" alt1="1H5*" alt2="1H5'"/>
<Atom name="H5''" alt1="2H5*"/> <Atom name="H5''" alt1="2H5*" atl2="2H5'"/>
<Atom name="HO2'" alt1="2HO*"/> <Atom name="HO2'" alt1="2HO*"/>
<Atom name="HO3'" alt1="H3T"/> <Atom name="HO3'" alt1="H3T"/>
<Atom name="HO5'" alt1="H5T"/>
</Residue> </Residue>
<Residue name="GLY" type="Protein"> <Residue name="GLY" type="Protein">
<Atom name="HA2" alt1="2HA"/> <Atom name="HA2" alt1="2HA"/>
...@@ -269,7 +270,7 @@ ...@@ -269,7 +270,7 @@
<Atom name="H72" alt1="2H5M"/> <Atom name="H72" alt1="2H5M"/>
<Atom name="H73" alt1="3H5M"/> <Atom name="H73" alt1="3H5M"/>
</Residue> </Residue>
<Residue name="HOH" alt1="H20" alt2="WAT" alt3="SOL" alt4="TIP3"> <Residue name="HOH" alt1="H20" alt2="WAT" alt3="SOL" alt4="TIP3" alt5="TP3">
<Atom name="O" alt1="OW" alt2="OH2"/> <Atom name="O" alt1="OW" alt2="OH2"/>
<Atom name="H1" alt1="HW1"/> <Atom name="H1" alt1="HW1"/>
<Atom name="H2" alt1="HW2"/> <Atom name="H2" alt1="HW2"/>
......
wrappers/python/simtk/openmm/app/data/residues.xml
View file @ aa4dad89
<Residues> <Residues>
<Residue name="A"> <Residue name="A">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/> <Bond from="C1'" to="N9"/>
...@@ -40,6 +40,7 @@ ...@@ -40,6 +40,7 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="ACE"> <Residue name="ACE">
<Bond from="C" to="CH3"/> <Bond from="C" to="CH3"/>
...@@ -154,7 +155,7 @@ ...@@ -154,7 +155,7 @@
<Bond from="HXT" to="OXT"/> <Bond from="HXT" to="OXT"/>
</Residue> </Residue>
<Residue name="C"> <Residue name="C">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/> <Bond from="C1'" to="N1"/>
...@@ -191,6 +192,7 @@ ...@@ -191,6 +192,7 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="CYS"> <Residue name="CYS">
<Bond from="-C" to="N"/> <Bond from="-C" to="N"/>
...@@ -210,7 +212,7 @@ ...@@ -210,7 +212,7 @@
<Bond from="HXT" to="OXT"/> <Bond from="HXT" to="OXT"/>
</Residue> </Residue>
<Residue name="DA"> <Residue name="DA">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/> <Bond from="C1'" to="N9"/>
...@@ -249,9 +251,10 @@ ...@@ -249,9 +251,10 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="DC"> <Residue name="DC">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/> <Bond from="C1'" to="N1"/>
...@@ -287,9 +290,10 @@ ...@@ -287,9 +290,10 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="DG"> <Residue name="DG">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/> <Bond from="C1'" to="N9"/>
...@@ -329,9 +333,10 @@ ...@@ -329,9 +333,10 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="DT"> <Residue name="DT">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/> <Bond from="C1'" to="N1"/>
...@@ -369,6 +374,7 @@ ...@@ -369,6 +374,7 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="FOR"> <Residue name="FOR">
<Bond from="-C" to="N"/> <Bond from="-C" to="N"/>
...@@ -378,7 +384,7 @@ ...@@ -378,7 +384,7 @@
<Bond from="H3" to="N"/> <Bond from="H3" to="N"/>
</Residue> </Residue>
<Residue name="G"> <Residue name="G">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N9"/> <Bond from="C1'" to="N9"/>
...@@ -419,6 +425,7 @@ ...@@ -419,6 +425,7 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="GLN"> <Residue name="GLN">
<Bond from="-C" to="N"/> <Bond from="-C" to="N"/>
...@@ -812,7 +819,7 @@ ...@@ -812,7 +819,7 @@
<Bond from="HXT" to="OXT"/> <Bond from="HXT" to="OXT"/>
</Residue> </Residue>
<Residue name="U"> <Residue name="U">
<Bond from="-OP3" to="P"/> <Bond from="-O3'" to="P"/>
<Bond from="C1'" to="C2'"/> <Bond from="C1'" to="C2'"/>
<Bond from="C1'" to="H1'"/> <Bond from="C1'" to="H1'"/>
<Bond from="C1'" to="N1"/> <Bond from="C1'" to="N1"/>
...@@ -848,6 +855,7 @@ ...@@ -848,6 +855,7 @@
<Bond from="OP1" to="P"/> <Bond from="OP1" to="P"/>
<Bond from="OP2" to="P"/> <Bond from="OP2" to="P"/>
<Bond from="OP3" to="P"/> <Bond from="OP3" to="P"/>
<Bond from="HO5'" to="O5'"/>
</Residue> </Residue>
<Residue name="UNK"> <Residue name="UNK">
<Bond from="-C" to="N"/> <Bond from="-C" to="N"/>
......
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