I did a docking and got a negative binding energy(-9.9kcal/mol) but after performing MM/PBSA for that same complex, I am getting 8323kJ/mol?

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Martin Klvana

Can you share a representative snapshot from the MD simulation?

Mario E. Valdés-Tresanco

Michael Afiadenyo I don't know what program are you using, but probably something is wrong with the trajectory... probably PBC?

have you tried gmx_MMPBSA?

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/getting-started/

Jasdeep Singh

Mario E. Valdés-Tresanco Does gmxMMPSA support gromos ff? If not, is there a way around to use gmxMMPSA for presimulated systems using gromos FFs. Thanks.

Jasdeep Singh unfortunately, gmx_MMPBSA does not support GROMOS yet... we plan to support this force field in the near future though

Thanks Mario E. Valdés-Tresanco . Looking forward to it !