Hello all,
I have molecular dynamic simulations of three membrane-peptide systems, and I want to calculate the free binding energy of the peptide to each membrane. Which method is more accurate for this kind of system? And, can you provide me with some tutorials I can follow? I tried using MM/GBSA following the discussion forum (https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2016-2017/0657.html) however I want to know if this is the best one for these systems or if I should use other? My simulations were performed using NAMD.
Thanks
Daniel
MMPBSA/GBSA works well with the protein-ligand system. For membrane-protein/peptide, potential mean force calculations or free energy perturbation could be performed. The following article might help
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054751/
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