Hey,
I was wondering if anybody has tried to upload a MOL2 file that was
generated with PyRED to CHARMM-GUI when preparing a Protein + Ligand
system.
I tried to do this but CHARMM-GUI always crashed. The reason for that
was apparently that the bond order in the MOL2 file generated by PyRED
does not match the requirements of CHARMM-GUI.
I would like to use the parameters generated by PyRED for the ligand and
simultaneously use the ff19SB ff for the protein and lipid21 for the
lipids that is provided by CHARMM-GUI.
Additionally, I want CHARMM-GUI to give me the output file in the
GROMACS format.
I already reached out the dev of PyRED and he would be also interested
in a possible solution.
Best
Eddie
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Received on Sun May 21 2023 - 07:00:02 PDT
