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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 > ________________________________________ > From: Ray Luo [rluo.uci.edu] > Sent: Sunday, March 13, 2016 4:21 AM > To: AMBER Mailing List > Subject: Re: [AMBER] How is ÄGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) > > Hi Stefan, > >> I would like to ask a few questions regarding MMPBSA.py's >> implementation in AMBER14. Having read the AMBER14 manual, the >> MMPBSA.py paper, and a few papers referenced in the manual, I'm a >> bit confused and unsure about a few things. >> >> What is the default scheme for computing ÄGsolvation in MMPBSA.py >> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)? >> I'm specifically talking about the Poisson-Boltzmann computations, i.e. >> inp=2 in the &pb namelist (which is equivalent to not specifying >> anything for inp, because 2 is the default value, right)?. I think the >> manual is a bit unclear. From what I understand > > This is correct. > >> ÄGsolvation = ÄGelectrostatic + ÄGnonpolar >> >> and >> >> ÄGnonpolar = ÄGrepulsive(ÄGcavitation) + ÄGattractive (ÄGdispersion). > > Yes, this is correct. > >> Finally: >> >> ÄGrepulsive = ã*SASA + c > > The default behavior is that the repulsive free energy is modeled as > linearly depended on the volume within SASA since this is the best > observed scheme for the tested small molecules and side chain mutation > data. > >> where SASA is computed with the LCPO method. Is this correct or is >> the cavitation term proportional to molecular volume? If so, how is that >> computed? > > If you choose to model it as linearly dependent on SASA, PBSA would > compute SASA numerically, it does not use the approximated LCPO > method. > >> Here is a typical output file I get (see below). I see EPB, ENPOLAR, >> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is >> the (repulsive) cavitation term and EDISPER is the (attractive) >> dispersion term (although in this case ENPOLAR is negative and >> ECAVITY is positive)? > > This is because the the printing of ECAVITY (inp=2) shares the same > routine as the printing ENPOLAR (inp=1) in the script. Again this is > because they both use linearly functional models. The sander printout > is more informative. > >> Also, is the internal PBSA solver in sander linear or nonlinear? > > It's linear by default. > >> I have seen a lot of recommendations for the "perl" version of >> MMPBSA, but very little for MMPBSA.py. What settings would you >> recommend for doing Poisson-Boltzmann calculations on protein - >> protein complexes? > > The two scripts should give you the same results if you use the same > options. The difference is that the perl script uses sander, and the > python script uses nab by default. If you prefer, you can use the > sander option in the python script so you can choose all the &pb > keywords as described in the manual. Apparently it is too hard to > support all &pb keywords in either scripts. > > You may want to use inp=1 for protein-protein complexes because the > inp=2 was not optimized for macromolecular "ligand" binding, though we > are working on it. > > All the best, > Ray > -- > Ray Luo, Ph.D. > Professor > Biochemistry, Molecular Biophysics, Chemical Physics, > Chemical and Biomedical Engineering > University of California, Irvine, CA 92697-3900 > > _______________________________________________ > 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/amber _______________________________________________ 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 Sun Mar 13 2016 - 22:30:03 PDT