Dear Ray,
Thank you very much for your help.
As I know the default surface tension coefficient is different for GB and PB, I used default parameters for GB and inp=1 parameters for PB.
Also, I performed energy decomposition and noticed that some amino acids, for instance, the N-terminal methionine, of GLY, PRO in some specific positions or the GTP molecule, can have very different contributions (~50 fold), for more details see the attached files.
Maybe this information can help solve this issue.
Nevertheless, which method is more reliable, or how it is possible to validate this data? I used normal mode, but it is too slow since my protein complexes have about 13000 atoms, what would recommend for protein-protein interaction free energy calculation?
Best regards,
Harutyun
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Received on Tue Oct 20 2020 - 06:00:02 PDT
