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Commit 839b1549 authored by peastman's avatar peastman
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Merge pull request #137 from peastman/master 

Fixed some errors in definitions of hydrogens
parents 85ed40c4 2f6a06ba
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Showing with 17 additions and 16 deletions
wrappers/python/simtk/openmm/app/data/hydrogens.xml
View file @ 839b1549
<Residues> <Residues>
<Residue name="A"> <Residue name="A">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2" parent="C2"/> <H name="H2" parent="C2"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
...@@ -11,7 +12,7 @@ ...@@ -11,7 +12,7 @@
<H name="H62" parent="N6"/> <H name="H62" parent="N6"/>
<H name="H8" parent="C8"/> <H name="H8" parent="C8"/>
<H name="HO2'" parent="O2'"/> <H name="HO2'" parent="O2'"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/> <H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/> <H name="HOP3" parent="OP3"/>
</Residue> </Residue>
...@@ -80,6 +81,7 @@ ...@@ -80,6 +81,7 @@
<H name="HD2" parent="OD2" maxph="4.4" variant="ASH"/> <H name="HD2" parent="OD2" maxph="4.4" variant="ASH"/>
</Residue> </Residue>
<Residue name="C"> <Residue name="C">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
<H name="H3'" parent="C3'"/> <H name="H3'" parent="C3'"/>
...@@ -91,7 +93,7 @@ ...@@ -91,7 +93,7 @@
<H name="H5''" parent="C5'"/> <H name="H5''" parent="C5'"/>
<H name="H6" parent="C6"/> <H name="H6" parent="C6"/>
<H name="HO2'" parent="O2'"/> <H name="HO2'" parent="O2'"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/> <H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/> <H name="HOP3" parent="OP3"/>
</Residue> </Residue>
...@@ -107,6 +109,7 @@ ...@@ -107,6 +109,7 @@
<H name="HG" parent="SG" maxph="8.5" variant="CYS"/> <H name="HG" parent="SG" maxph="8.5" variant="CYS"/>
</Residue> </Residue>
<Residue name="DA"> <Residue name="DA">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2" parent="C2"/> <H name="H2" parent="C2"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
...@@ -118,11 +121,10 @@ ...@@ -118,11 +121,10 @@
<H name="H61" parent="N6"/> <H name="H61" parent="N6"/>
<H name="H62" parent="N6"/> <H name="H62" parent="N6"/>
<H name="H8" parent="C8"/> <H name="H8" parent="C8"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/>
</Residue> </Residue>
<Residue name="DC"> <Residue name="DC">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
<H name="H2''" parent="C2'"/> <H name="H2''" parent="C2'"/>
...@@ -134,11 +136,10 @@ ...@@ -134,11 +136,10 @@
<H name="H5'" parent="C5'"/> <H name="H5'" parent="C5'"/>
<H name="H5''" parent="C5'"/> <H name="H5''" parent="C5'"/>
<H name="H6" parent="C6"/> <H name="H6" parent="C6"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/>
</Residue> </Residue>
<Residue name="DG"> <Residue name="DG">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1" parent="N1"/> <H name="H1" parent="N1"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
...@@ -150,11 +151,10 @@ ...@@ -150,11 +151,10 @@
<H name="H5'" parent="C5'"/> <H name="H5'" parent="C5'"/>
<H name="H5''" parent="C5'"/> <H name="H5''" parent="C5'"/>
<H name="H8" parent="C8"/> <H name="H8" parent="C8"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/>
</Residue> </Residue>
<Residue name="DT"> <Residue name="DT">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
<H name="H2''" parent="C2'"/> <H name="H2''" parent="C2'"/>
...@@ -167,15 +167,14 @@ ...@@ -167,15 +167,14 @@
<H name="H71" parent="C7"/> <H name="H71" parent="C7"/>
<H name="H72" parent="C7"/> <H name="H72" parent="C7"/>
<H name="H73" parent="C7"/> <H name="H73" parent="C7"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/>
</Residue> </Residue>
<Residue name="FOR"> <Residue name="FOR">
<H name="H1" parent="C"/> <H name="H1" parent="C"/>
<H name="H2" parent="C"/> <H name="H2" parent="C"/>
</Residue> </Residue>
<Residue name="G"> <Residue name="G">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1" parent="N1"/> <H name="H1" parent="N1"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
...@@ -187,7 +186,7 @@ ...@@ -187,7 +186,7 @@
<H name="H5''" parent="C5'"/> <H name="H5''" parent="C5'"/>
<H name="H8" parent="C8"/> <H name="H8" parent="C8"/>
<H name="HO2'" parent="O2'"/> <H name="HO2'" parent="O2'"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/> <H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/> <H name="HOP3" parent="OP3"/>
</Residue> </Residue>
...@@ -409,6 +408,7 @@ ...@@ -409,6 +408,7 @@
<H name="HH" parent="OH"/> <H name="HH" parent="OH"/>
</Residue> </Residue>
<Residue name="U"> <Residue name="U">
<H name="HO5'" parent="O5'" terminal="N"/>
<H name="H1'" parent="C1'"/> <H name="H1'" parent="C1'"/>
<H name="H2'" parent="C2'"/> <H name="H2'" parent="C2'"/>
<H name="H3" parent="N3"/> <H name="H3" parent="N3"/>
...@@ -419,7 +419,7 @@ ...@@ -419,7 +419,7 @@
<H name="H5''" parent="C5'"/> <H name="H5''" parent="C5'"/>
<H name="H6" parent="C6"/> <H name="H6" parent="C6"/>
<H name="HO2'" parent="O2'"/> <H name="HO2'" parent="O2'"/>
<H name="HO3'" parent="O3'"/> <H name="HO3'" parent="O3'" terminal="C"/>
<H name="HOP2" parent="OP2"/> <H name="HOP2" parent="OP2"/>
<H name="HOP3" parent="OP3"/> <H name="HOP3" parent="OP3"/>
</Residue> </Residue>
......
wrappers/python/simtk/openmm/app/data/residues.xml
View file @ 839b1549
...@@ -718,6 +718,7 @@ ...@@ -718,6 +718,7 @@
<Bond from="CG" to="HG2"/> <Bond from="CG" to="HG2"/>
<Bond from="CG" to="HG3"/> <Bond from="CG" to="HG3"/>
<Bond from="H" to="N"/> <Bond from="H" to="N"/>
<Bond from="H2" to="N"/>
<Bond from="H3" to="N"/> <Bond from="H3" to="N"/>
<Bond from="HXT" to="OXT"/> <Bond from="HXT" to="OXT"/>
</Residue> </Residue>
......
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