How to create the index file in accordance with this protocol?

tubiana / protocolGromacs

Automatic gromacs protocol from preparation to production with ligand parametrization through

MIT License

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Closed vmevada102 closed 8 months ago

vmevada102 commented 9 months ago

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.

tubiana commented 9 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.