leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
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Ligpargen produces Torsions with all k=0.00000 in OpenMM .xml file #49

Open bkpgh opened 4 years ago

bkpgh commented 4 years ago

Using the web server on multicyclic molecules, the OpenMM .xml file contains some torsions that have all of the force constants = 0.00000.

A simple example is DABCO (smiles=C1CN2CCN1CC2) for which the output contains lines including:

Improper... class1="C807" class2="N802" class3="H819" class4="C806" k1="0.000000" k2="0.000000" k3="0.000000" k4="0.000000" ...

For some other molecules, both Proper and Improper torsions like this appear.

Are these non-functional torsions evidence of

  1. a bug: there should be non-zero k's in there
  2. torsions that should have parameters, but they just don't exist in OPLS-AA
  3. torsions that resulted from a search, don't exist in OPLS-AA, aren't needed, and they can be deleted.
  4. Something else?