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-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Tue, Oct 20, 2015 at 6:46 AM, Jason Swails <jason.swails.gmail.com> wrote: > On Tue, Oct 20, 2015 at 6:01 AM, MarcZhang <progress0935zhang.gmail.com> > wrote: > >> Hi Jason >> >> >> >> Thanks a lot for your suggestions! >> >> >> >> I re-ran the calculation by adding inp=1, radiopt=0 into the PB section. >> >> >> >> The results showed that DELTA TOTAL (-90.8091) of the Differences (Complex >> - >> Receptor - Ligand) is much closer to the value (-86.3579) given in tutorial >> 3.1. >> >> >> >> However, TOTAL energy values of Complex, Receptor, and Ligand is still >> greatly deviated from the ones in the tutorial. >> > > Define "greatly deviated". 10 kcal/mol? More? Less? > > > >> Did I miss something in my calculations? What are the causes of this >> deviation? >> > > I'm really not entirely sure. I suspect different default settings in the > PB solver, but it's been a very long time since I've generated the results > for that tutorial (I should probably update it). One thing to keep in mind > is that only energy differences matter in MM calculations, though, so the > fact that the results are much closer is encouraging. > > Also, look at *where* the differences are. Is it all in the non-polar > solvation part? If so (and I suspect it is), then it's likely caused by > different surface tension defaults between the two versions, which > introduces bigger discrepancies in each system that tend to cancel to a > large degree when taking the difference. > > HTH, > Jason > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > _______________________________________________ > 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 2015 - 12:30:03 PDT