Closed vmevada102 closed 8 months ago
Hi!
To generate an index file you need to use gmx make_ndx
. You can have an usage example on my script here : https://github.com/tubiana/protocolGromacs/blob/a1665af4b6e37a142fd316c8b1b3aa54a33a8fac/runGromacs.sh#L132
I cannot help you more on your issue since I lack a bit of details and I never used MMGBSA with gromacs so I'm not sure what input you need.
Best regards, Thibault.
This protocol is excellent to the new bees like me.
However, I need little more support. I would like to run the MMPBSA after this run. For that, it is required to add index file.
Kindly guide to generate this file during this protocol run for Protein-ligand complex.