GROMACS version: 2022.3
GROMACS modification: No
Hi everyone,
I have a question about using gromacs for calculating the binding affinity between two proteins (overall my system has about 1600 amino acids). I was thinking about using gmx_MMPBSA and MMPBSA.py. Is it suitable for binding affinity calculation between 2 proteins? Or does it work well only for a system with a protein and a small ligand?
If using these tools is a good choice, I was wondering how long it is recommended to run the MDS. I know that is something specific and I expect it to change depending on the type of proteins, but I did not find anything in literature similar to my situation and I have read a pretty big range of simulation time between different simulations (about from 50 ns to 600 ns and more). So, I was wondering if there is a minimum simulation time that was observed to be necessary to obtain information about the binding affinity (maybe depending on the size of the proteins). And if you have other recommendations for correctly measuring binding affinity please let me know.
Thank you very much,
Martina