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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]: running MMPBSA by gromos forcefield toplogy and gromacs 2023.2 #543

Closed benyamin-moraditabar closed 2 weeks ago

benyamin-moraditabar commented 2 weeks ago

My Question is...

Hi, I have ran a protein-peptide simulation by gromacs 2023.2 and gromos 43a1.ff forcefield for parametrization.

Now I can't run gmx_mmpbsa because I came across this Error: Not all bond parameters found.

So how can I calculate the binding free energy with my xtc trajectory files generated by this version of gromacs and gromos forcefield???

Thanks for your attention.

Valdes-Tresanco-MS commented 2 weeks ago

Unfortunately, GROMOS is not supported. We will try to make it work in new versions implementing other programs and methods for PB.

benyamin-moraditabar commented 2 weeks ago

Unfortunately, GROMOS is not supported. We will try to make it work in new versions implementing other programs and methods for PB. Do you know how can I calculate the binding energy with other ways? would you please give me any clue for performing binding energy calculation?

Valdes-Tresanco-MS commented 2 weeks ago

You can perform the MD using Amber or CHARMM ff and then use gmx_MMPBSA. You can also use the LIE-based approach to calculate BFE. I don't remember if g_mmpbsa or GMXPBSA can use GROMOS, but you can check if they do. Other methods require the calculation again and can require a lot of computational resources.

benyamin-moraditabar commented 2 weeks ago

Thank you so much I will do all.