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leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
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Local Version of LigParGen lacks some Improper Dihedral parameters #92

Open wutobias opened 2 years ago

wutobias commented 2 years ago

Issue Information

Software name & Version : LigParGen in conda env. See attached ligpargen.yaml for info installed packages. [ligpargen.yaml.zip (https://github.com/leelasd/ligpargen/files/8043766/ligpargen.yaml.zip)

Method: Running locally LigParGen -s 'C(=O)(C(=O)N)N' -o 0 -c 0 -r M0 and running same smiles on the LigParGen server

Expected Behavior

The LigParGen server generates the seemingly correct the improper dihedral potentials parameters. This is the expected behaviour.

<Improper class1="N801" class2="H800" class3="C802" class4="H803" k1="0.000000" k2="10.460000" k3="0.000000" k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00" phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>
<Improper class1="N806" class2="H808" class3="H809" class4="C804" k1="0.000000" k2="10.460000" k3="0.000000" k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00" phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>
<Improper class1="C802" class2="N801" class3="C804" class4="O805" k1="0.000000" k2="43.932000" k3="0.000000" k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00" phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>
<Improper class1="C804" class2="C802" class3="N806" class4="O807" k1="0.000000" k2="43.932000" k3="0.000000" k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00" phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>

Actual Behavior

The locally installed version of the program generates the following output. Effectively missing half of the improper dihedrals.

<Improper class1="C802" class2="C800" class3="O803" class4="N804" k1="0.000000" k2="43.932000" k3="0.000000" k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00" phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>
<Improper class1="C800" class2="N805" class3="O801" class4="C802" k1="0.000000" k2="43.932000" k3="0.000000" k4="0.000000" periodicity1="1" periodicity2="2" periodicity3="3" periodicity4="4" phase1="0.00" phase2="3.141592653589793" phase3="0.00" phase4="3.141592653589793"/>

I suspect that this bug was resolved in the server version but not passed down to the local version. If this is the case, is there any chance you could update the packaged version available via pip?

wutobias commented 2 years ago

Attaching the ligpargen.yaml file to reproduce the conda env

ligpargen.yaml.zip