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luancarvalhomartins / PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
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Problems with using Cgenff topologies #116

Closed pallavsen007 closed 1 year ago

pallavsen007 commented 1 year ago

Most of the CGenFF topologies are built using mol2 files to get the str and itp files respectively. And after that if one has to go through the PyAutoFEP tool, one essentially has to build 'mol' files again especially from SMILES which is convenient using this tool, but again there are problems with the atom naming. It would be wise to parameterize directly from the mol files to get cgenff topologies then build the dual topology using 'prepare_dual_topology'.

luancarvalhomartins commented 1 year ago

Sorry, I did not quite follow your suggestion.

PyAutoFEP is able to handle .mol2 files. The recommended way to use CGenFF topologies is to parameterize your molecules then pass the output .str and .mol2 files to prepare_dual_topology.py. See the manual, section 3.3, for more info.

pallavsen007 commented 1 year ago

ok. I was misunderstanding it. Thanks a lot. You may close the issue.

luancarvalhomartins commented 1 year ago

Thank you very much and feel free to file a new issue should you need any further assistance!