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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Question]: Protein-membrane per residue decomposition #421

Closed margretheg closed 11 months ago

margretheg commented 11 months ago

My Question is...

I want to use gmx_MMPBSA to analyse a protein-protein complex where the receptor is embedded in a lipid bilayer. I've used the CHARMM36 ff for the simulations, and followed your tutorial (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Protein_membrane_CHARMMff/). This seems to work fine! However, I would also like to include per-residue decomposition. Is this valid for protein-membrane systems? I only want to look at the residues in the protein complex, and treat the membrane implicitly. If valid, which option should I use for idecomp, 1 or 2? Or does it not matter? Thanks a lot for answers!

marioernestovaldes commented 11 months ago

yes, you can use it for decomposition... you can use idecomp=2... more info here:

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/#decomp-namelist-variables

margretheg commented 11 months ago

Thanks a lot for the quick response!