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CCPBioSim / fesetup

A tool for setting up free energy simulations.
http://www.ccpbiosim.ac.uk/software
GNU General Public License v2.0
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ligand charges #6

Open skfegan opened 6 years ago

skfegan commented 6 years ago

FESetup struggles to get the correct charge for positive and negatively charged ligands. It seems like this can also cause trouble with the complexes.

edwardclem commented 5 years ago

I'm experiencing this bug as well - I believe it's caused by a bug in pybel with identifying charges in .mol2 files. Converting files to .mol format (with RDKit) has so far resolved this problem for me.

skfegan commented 5 years ago

Thanks @edwardclem. If you want to contribute a fix for FESetup, you are welcome to do that. Please submit any pull requests to the dev branch (the master branch is for released versions).

edwardclem commented 5 years ago

Okay, gotcha! I submitted a bug report to the openbabel devs, seems like charge issues are fairly well known to them. Fixing it through that route seems like the best option to minimize changes to the FESetup code, without adding additional charge-checking code on top of pybel or switching the internal mol processing library from pybel to RDKit, for example.