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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Tue, Oct 20, 2020 at 5:29 AM <h_sahakyan.mb.sci.am> wrote: > > 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 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Oct 20 2020 - 10:00:04 PDT