add test to catch bugs in improper dihedrals handling [WIP]

nhenriksen / speakeasy

Automates the conversion of SMIRNOFF parameters to AMBER force field files

MIT License

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Closed jaimergp closed 4 years ago

jaimergp commented 4 years ago

First draft to catch those problems with dihedrals.

Several things going on:

We have to provide atom and residue names so ParmEd/tleap can work
ParmEd must be monkey patched to catch the right central atom
Scaling factors in dihedrals are not set properly, so we are specifying those manually for all dihedral types. Is there any way to do this in a smarter way?