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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Mon, Dec 2, 2013 at 3:52 PM, <psu4.uic.edu> wrote: > Dear Professor Luo, > > Thanks for your explanation. Will look forward the next Amber 14(?!). > > Henry > > > On Mon, Nov 18, 2013 at 6:09 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: > > > Henry, > > > > MMPBSA actually uses the radii values in the prmtop files when > > INP=1/radiopt=0. These are mbondi or mbondi2 radii. They are similar > > to parse radii, but not the same, particularly those for the hydrogen > > atoms. PBSA will support the pqr format in the next year's release. > > When the new version is ready, you can use whatever radii in your pqr > > files. > > > > Ray > > -- > > Ray Luo, Ph.D. > > Professor, > > Biochemistry, Molecular Biophysics, and > > Biomedical Engineering > > University of California, Irvine, CA 92697-3900 > > > > > > On Mon, Nov 18, 2013 at 3:50 PM, <psu4.uic.edu> wrote: > > > Dear Amber, > > > > > > > > > > > > After reading the PARSE radii paper (J . Phys. Chem. 1994,98, > > 1978-1988), > > > some other related papers, and previous mailing lists, ( > > > http://archive.ambermd.org/201208/0085.html, > > > http://archive.ambermd.org/201308/0044.html , > > > http://archive.ambermd.org/201006/0531.html, > > > http://archive.ambermd.org/200704/0071.html, > > > http://archive.ambermd.org/201007/0594.html, > > > http://archive.ambermd.org/201006/0132.html ), we are still a bit > > confused. > > > > > > > > > > > > > > > > > > MM/PBSA: According to the MMPBSA.py manual, if inp=1 and radiopt=0, > it > > > seems like MMPBSA.py uses PARSE radii for the non-polar solvation > energy > > > terms. However, a simple test in MM/PBSA using different prmtop in > > > various effective radii (bondi, mbondi, mbondi2) gives a slightly > > different > > > non-polar energy values. Is it because inp=1 and radiopt =0 forces > > > MMPBSA.py to overwrite effective radii (bondi, mbondi, mbondi2) over > > PARSE > > > radii? > > > > > > > > > > > > MM/PBSA test results: 250 ps, inp=1, radiopt=0, > > > > > > Bondi > > > > > > ÄGvdw > > > > > > ÄGelec > > > > > > *ÄGpb* > > > > > > *ÄGnon-polar* > > > > > > bondi > > > > > > -35.15 > > > > > > -15.15 > > > > > > *30.20* > > > > > > *-2.3989* > > > > > > mbondi > > > > > > -35.15 > > > > > > -15.15 > > > > > > *32.38* > > > > > > *-2.4313* > > > > > > mbondi2 > > > > > > -35.15 > > > > > > -15.15 > > > > > > *30.12* > > > > > > *-2.3972* > > > > > > > > > > > > > > > > > > In MM/GBSA in MMPBSA.py, different effective radii settings (bondi, > > mbondi, > > > mbondi2) will affect dG(GB) for sure, as reported by various > literatures > > > (igb =1,2,5,7,8 original publications). However, unlike the scenario > in > > > MM/PBSA, wonder why Amber default settings force MM/GBSA non-sensitive > to > > > the non-polar term (deltaGNPOLAR)? > > > > > > > > > > > > MM/GBSA test results, 250 ps > > > > > > Bondi > > > > > > deltaGVDW > > > > > > deltaGelec > > > > > > *deltaGPBb* > > > > > > *deltaGNPOLAR* > > > > > > deltaGsolvation > > > > > > deltaGBinding > > > > > > bondi > > > > > > -35.1465 > > > > > > -15.1476 > > > > > > *20.5781* > > > > > > *-4.4684* > > > > > > 16.1097 > > > > > > -34.1844 > > > > > > mbondi > > > > > > -35.1465 > > > > > > -15.1476 > > > > > > *22.5793* > > > > > > *-4.4684* > > > > > > 18.1109 > > > > > > -32.1832 > > > > > > mbondi2 > > > > > > -35.1465 > > > > > > -15.1476 > > > > > > *19.961* > > > > > > *-4.4684* > > > > > > 15.4926 > > > > > > -34.8015 > > > > > > > > > > > > Cheers, > > > > > > Henry > > > _______________________________________________ > > > 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 > > > > > > -- > > Pin-Chih Su (Henry Su) > > Ph.D. canditate > > Center for Pharmaceutical Biotechnology (MC 870) > > College of Pharmacy, University of Illinois at Chicago > > 900 South Ashland Avenue, Room 1052 > > Chicago, IL 60607-7173 > > office 312-996-5388 > > fax 312-413-9303 > _______________________________________________ > 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 Mon Dec 02 2013 - 17:00:02 PST