Fixes and extensions for ligand parameterization

choderalab / protons

OpenMM testbed for constant-pH methodologies.

http://protons.readthedocs.io/

MIT License

20 stars 13 forks source link

Closed bas-rustenburg closed 5 years ago

bas-rustenburg commented 5 years ago

Based on previous issues with parametrizing viologen as a molecule, this PR implements some workarounds / fixes, namely:

dense conformer sampling by omega for molecules where AM1BCC is hard to converge
A workaround for odd formal charges by patching an intermediate mol2 file with integer bonds.