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Unverified Commit 2f20fbe2 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Fixed error using AMOEBA 2018 with RNA (#3313)

parent edee11b6
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Showing with 820 additions and 403 deletions
devtools/forcefield-scripts/residuesFinal.xml
View file @ 2f20fbe2
...@@ -2030,7 +2030,7 @@ ...@@ -2030,7 +2030,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -2100,7 +2100,7 @@ ...@@ -2100,7 +2100,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -2170,7 +2170,7 @@ ...@@ -2170,7 +2170,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -2236,7 +2236,7 @@ ...@@ -2236,7 +2236,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
...@@ -2304,7 +2304,7 @@ ...@@ -2304,7 +2304,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -2369,7 +2369,7 @@ ...@@ -2369,7 +2369,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -2434,7 +2434,7 @@ ...@@ -2434,7 +2434,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -2495,7 +2495,7 @@ ...@@ -2495,7 +2495,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
...@@ -2563,7 +2563,7 @@ ...@@ -2563,7 +2563,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -2635,7 +2635,7 @@ ...@@ -2635,7 +2635,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -2707,7 +2707,7 @@ ...@@ -2707,7 +2707,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -2775,7 +2775,7 @@ ...@@ -2775,7 +2775,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
...@@ -2843,7 +2843,7 @@ ...@@ -2843,7 +2843,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
<Bond from="P" to="O2P"/> <Bond from="P" to="O2P"/>
...@@ -2906,7 +2906,7 @@ ...@@ -2906,7 +2906,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="P" to="O1P"/> <Bond from="P" to="O1P"/>
...@@ -2969,7 +2969,7 @@ ...@@ -2969,7 +2969,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
<Bond from="O5'" to="C5'"/> <Bond from="O5'" to="C5'"/>
...@@ -3028,7 +3028,7 @@ ...@@ -3028,7 +3028,7 @@
<Atom name="C2'" tinkerLookupName="C2*"/> <Atom name="C2'" tinkerLookupName="C2*"/>
<Atom name="H2'" tinkerLookupName="H2*"/> <Atom name="H2'" tinkerLookupName="H2*"/>
<Atom name="O2'" tinkerLookupName="O2*"/> <Atom name="O2'" tinkerLookupName="O2*"/>
<Atom name="HO2'" tinkerLookupName="H2*"/> <Atom name="HO2'" tinkerLookupName="HO*"/>
<Atom name="O3'" tinkerLookupName="O3*"/> <Atom name="O3'" tinkerLookupName="O3*"/>
<Atom name="H3T" tinkerLookupName="H3T"/> <Atom name="H3T" tinkerLookupName="H3T"/>
<Bond from="H5T" to="O5'"/> <Bond from="H5T" to="O5'"/>
......
wrappers/python/openmm/app/data/amoeba2018.xml
View file @ 2f20fbe2
<ForceField> <ForceField>
<Info> <Info>
<Source>amoebabio18.prm</Source> <Source>amoebabio18.prm</Source>
<DateGenerated>2021-11-02</DateGenerated> <DateGenerated>2021-11-04</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> <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>
<Reference>Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, Jay W Ponder, and Pengyu Ren. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. Journal of Chemical Theory and Computation, 14(4):2084-2108, 2018.</Reference> <Reference>Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, Jay W Ponder, and Pengyu Ren. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. Journal of Chemical Theory and Computation, 14(4):2084-2108, 2018.</Reference>
</Info> </Info>
...@@ -4325,7 +4325,7 @@ ...@@ -4325,7 +4325,7 @@
<Atom name="H61" type="260" /> <Atom name="H61" type="260" />
<Atom name="H62" type="260" /> <Atom name="H62" type="260" />
<Atom name="H8" type="258" /> <Atom name="H8" type="258" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="257" /> <Atom name="N1" type="257" />
<Atom name="N3" type="256" /> <Atom name="N3" type="256" />
<Atom name="N6" type="253" /> <Atom name="N6" type="253" />
...@@ -4398,7 +4398,7 @@ ...@@ -4398,7 +4398,7 @@
<Atom name="H61" type="260" /> <Atom name="H61" type="260" />
<Atom name="H62" type="260" /> <Atom name="H62" type="260" />
<Atom name="H8" type="258" /> <Atom name="H8" type="258" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="257" /> <Atom name="N1" type="257" />
<Atom name="N3" type="256" /> <Atom name="N3" type="256" />
<Atom name="N6" type="253" /> <Atom name="N6" type="253" />
...@@ -4471,7 +4471,7 @@ ...@@ -4471,7 +4471,7 @@
<Atom name="H61" type="260" /> <Atom name="H61" type="260" />
<Atom name="H62" type="260" /> <Atom name="H62" type="260" />
<Atom name="H8" type="258" /> <Atom name="H8" type="258" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="257" /> <Atom name="N1" type="257" />
<Atom name="N3" type="256" /> <Atom name="N3" type="256" />
<Atom name="N6" type="253" /> <Atom name="N6" type="253" />
...@@ -4539,7 +4539,7 @@ ...@@ -4539,7 +4539,7 @@
<Atom name="H61" type="260" /> <Atom name="H61" type="260" />
<Atom name="H62" type="260" /> <Atom name="H62" type="260" />
<Atom name="H8" type="258" /> <Atom name="H8" type="258" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="257" /> <Atom name="N1" type="257" />
<Atom name="N3" type="256" /> <Atom name="N3" type="256" />
<Atom name="N6" type="253" /> <Atom name="N6" type="253" />
...@@ -4604,7 +4604,7 @@ ...@@ -4604,7 +4604,7 @@
<Atom name="H5'" type="325" /> <Atom name="H5'" type="325" />
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H6" type="271" /> <Atom name="H6" type="271" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="261" /> <Atom name="N1" type="261" />
<Atom name="N3" type="268" /> <Atom name="N3" type="268" />
<Atom name="N4" type="264" /> <Atom name="N4" type="264" />
...@@ -4672,7 +4672,7 @@ ...@@ -4672,7 +4672,7 @@
<Atom name="H5'" type="325" /> <Atom name="H5'" type="325" />
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H6" type="271" /> <Atom name="H6" type="271" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="261" /> <Atom name="N1" type="261" />
<Atom name="N3" type="268" /> <Atom name="N3" type="268" />
<Atom name="N4" type="264" /> <Atom name="N4" type="264" />
...@@ -4740,7 +4740,7 @@ ...@@ -4740,7 +4740,7 @@
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H5T" type="327" /> <Atom name="H5T" type="327" />
<Atom name="H6" type="271" /> <Atom name="H6" type="271" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="261" /> <Atom name="N1" type="261" />
<Atom name="N3" type="268" /> <Atom name="N3" type="268" />
<Atom name="N4" type="264" /> <Atom name="N4" type="264" />
...@@ -4803,7 +4803,7 @@ ...@@ -4803,7 +4803,7 @@
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H5T" type="327" /> <Atom name="H5T" type="327" />
<Atom name="H6" type="271" /> <Atom name="H6" type="271" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="261" /> <Atom name="N1" type="261" />
<Atom name="N3" type="268" /> <Atom name="N3" type="268" />
<Atom name="N4" type="264" /> <Atom name="N4" type="264" />
...@@ -4865,7 +4865,7 @@ ...@@ -4865,7 +4865,7 @@
<Atom name="H5'" type="325" /> <Atom name="H5'" type="325" />
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H8" type="286" /> <Atom name="H8" type="286" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="277" /> <Atom name="N1" type="277" />
<Atom name="N2" type="278" /> <Atom name="N2" type="278" />
<Atom name="N3" type="283" /> <Atom name="N3" type="283" />
...@@ -4940,7 +4940,7 @@ ...@@ -4940,7 +4940,7 @@
<Atom name="H5'" type="325" /> <Atom name="H5'" type="325" />
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H8" type="286" /> <Atom name="H8" type="286" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="277" /> <Atom name="N1" type="277" />
<Atom name="N2" type="278" /> <Atom name="N2" type="278" />
<Atom name="N3" type="283" /> <Atom name="N3" type="283" />
...@@ -5015,7 +5015,7 @@ ...@@ -5015,7 +5015,7 @@
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H5T" type="327" /> <Atom name="H5T" type="327" />
<Atom name="H8" type="286" /> <Atom name="H8" type="286" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="277" /> <Atom name="N1" type="277" />
<Atom name="N2" type="278" /> <Atom name="N2" type="278" />
<Atom name="N3" type="283" /> <Atom name="N3" type="283" />
...@@ -5085,7 +5085,7 @@ ...@@ -5085,7 +5085,7 @@
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H5T" type="327" /> <Atom name="H5T" type="327" />
<Atom name="H8" type="286" /> <Atom name="H8" type="286" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="277" /> <Atom name="N1" type="277" />
<Atom name="N2" type="278" /> <Atom name="N2" type="278" />
<Atom name="N3" type="283" /> <Atom name="N3" type="283" />
...@@ -5151,7 +5151,7 @@ ...@@ -5151,7 +5151,7 @@
<Atom name="H5'" type="325" /> <Atom name="H5'" type="325" />
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H6" type="310" /> <Atom name="H6" type="310" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="304" /> <Atom name="N1" type="304" />
<Atom name="N3" type="303" /> <Atom name="N3" type="303" />
<Atom name="O1P" type="344" /> <Atom name="O1P" type="344" />
...@@ -5217,7 +5217,7 @@ ...@@ -5217,7 +5217,7 @@
<Atom name="H5'" type="325" /> <Atom name="H5'" type="325" />
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H6" type="310" /> <Atom name="H6" type="310" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="304" /> <Atom name="N1" type="304" />
<Atom name="N3" type="303" /> <Atom name="N3" type="303" />
<Atom name="O1P" type="344" /> <Atom name="O1P" type="344" />
...@@ -5283,7 +5283,7 @@ ...@@ -5283,7 +5283,7 @@
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H5T" type="327" /> <Atom name="H5T" type="327" />
<Atom name="H6" type="310" /> <Atom name="H6" type="310" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="304" /> <Atom name="N1" type="304" />
<Atom name="N3" type="303" /> <Atom name="N3" type="303" />
<Atom name="O2" type="308" /> <Atom name="O2" type="308" />
...@@ -5344,7 +5344,7 @@ ...@@ -5344,7 +5344,7 @@
<Atom name="H5''" type="325" /> <Atom name="H5''" type="325" />
<Atom name="H5T" type="327" /> <Atom name="H5T" type="327" />
<Atom name="H6" type="310" /> <Atom name="H6" type="310" />
<Atom name="HO2'" type="317" /> <Atom name="HO2'" type="321" />
<Atom name="N1" type="304" /> <Atom name="N1" type="304" />
<Atom name="N3" type="303" /> <Atom name="N3" type="303" />
<Atom name="O2" type="308" /> <Atom name="O2" type="308" />
......
wrappers/python/openmm/app/data/amoeba2018_gk.xml
View file @ 2f20fbe2
<ForceField> <ForceField>
<Info> <Info>
<Source>amoebabio18.prm</Source> <Source>amoebabio18.prm</Source>
<DateGenerated>2021-11-02</DateGenerated> <DateGenerated>2021-11-04</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> <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>
<Reference>Rae A. Corrigan, Guowei Qi, Andrew C. Thiel, Jack R. Lynn, Brandon D. Walker, Thomas L. Casavant, Louis Lagardere, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Ren, and Michael J. Schnieders. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation, 17(4):2323-2341, 2021.</Reference> <Reference>Rae A. Corrigan, Guowei Qi, Andrew C. Thiel, Jack R. Lynn, Brandon D. Walker, Thomas L. Casavant, Louis Lagardere, Jean-Philip Piquemal, Jay W. Ponder, Pengyu Ren, and Michael J. Schnieders. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation, 17(4):2323-2341, 2021.</Reference>
</Info> </Info>
......
wrappers/python/tests/TestForceField.py
View file @ 2f20fbe2
...@@ -1345,23 +1345,23 @@ class AmoebaTestForceField(unittest.TestCase): ...@@ -1345,23 +1345,23 @@ class AmoebaTestForceField(unittest.TestCase):
self.assertAlmostEqual(-1323.5640-225.3660, energies['AmoebaMultipoleForce'], 2) self.assertAlmostEqual(-1323.5640-225.3660, energies['AmoebaMultipoleForce'], 2)
self.assertAlmostEqual(-258.9676, sum(list(energies.values())), 2) self.assertAlmostEqual(-258.9676, sum(list(energies.values())), 2)
def test_Amoeba18DNA(self): def test_Amoeba18Nucleic(self):
"""Test that AMOEBA18 computes energies correctly for DNA.""" """Test that AMOEBA18 computes energies correctly for DNA and RNA."""
energies = self.computeAmoeba18Energies('systems/dna.pdb') energies = self.computeAmoeba18Energies('systems/nucleic.pdb')
# Compare to values computed with Tinker. # Compare to values computed with Tinker.
self.assertAlmostEqual(688.7794, energies['AmoebaBond'], 4) self.assertAlmostEqual(749.6953, energies['AmoebaBond'], 4)
self.assertAlmostEqual(430.5887, energies['AmoebaAngle']+energies['AmoebaInPlaneAngle'], 4) self.assertAlmostEqual(579.9971, energies['AmoebaAngle']+energies['AmoebaInPlaneAngle'], 4)
self.assertAlmostEqual(10.5715, energies['AmoebaOutOfPlaneBend'], 4) self.assertAlmostEqual(10.6630, energies['AmoebaOutOfPlaneBend'], 4)
self.assertAlmostEqual(0.7773, energies['AmoebaStretchBend'], 4) self.assertAlmostEqual(5.2225, energies['AmoebaStretchBend'], 4)
self.assertAlmostEqual(77.0482, energies['PeriodicTorsionForce'], 4) self.assertAlmostEqual(166.7233, energies['PeriodicTorsionForce'], 4)
self.assertAlmostEqual(56.5654, energies['AmoebaPiTorsion'], 4) self.assertAlmostEqual(57.2066, energies['AmoebaPiTorsion'], 4)
self.assertAlmostEqual(-0.5457, energies['AmoebaStretchTorsion'], 4) self.assertAlmostEqual(-4.2538, energies['AmoebaStretchTorsion'], 4)
self.assertAlmostEqual(-1.6044, energies['AmoebaAngleTorsion'], 4) self.assertAlmostEqual(-5.0402, energies['AmoebaAngleTorsion'], 4)
self.assertAlmostEqual(106.4062, energies['AmoebaVdwForce'], 4) self.assertAlmostEqual(187.1103, energies['AmoebaVdwForce'], 4)
self.assertAlmostEqual(90.5715-73.6051, energies['AmoebaMultipoleForce'], 4) self.assertAlmostEqual(1635.1289-236.1484, energies['AmoebaMultipoleForce'], 3)
self.assertAlmostEqual(1385.5529, sum(list(energies.values())), 4) self.assertAlmostEqual(3146.3046, sum(list(energies.values())), 3)
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/dna.pdb deleted 100644 → 0
View file @ edee11b6
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wrappers/python/tests/systems/nucleic.pdb 0 → 100644
View file @ 2f20fbe2
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