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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Wed, Jun 19, 2019 at 10:51 PM Ray Luo <rluo.uci.edu> wrote: > > Thomas, > > Thanks a lot for reporting! Let me take a look ... > > All the best, > Ray > -- > Ray Luo, Ph.D. > Professor of Structural Biology/Biochemistry/Biophysics, > Chemical Physics, Biomedical Engineering, and Chemical Engineering > Department of Molecular Biology and Biochemistry > University of California, Irvine, CA 92697-3900 > > On Wed, Jun 19, 2019 at 10:49 PM Thomas Gaillard > <thomas.gaillard.polytechnique.edu> wrote: > > > > Hi Ray, > > > > Thanks for your answer. The problem is not limited to MMPBSA.py but is > > in the pbsa code. > > > > I have sent a more detailed bug report and solution: > > > > http://archive.ambermd.org/201906/0179.html > > > > Best regards, > > > > Thomas Gaillard > > > > Le Tuesday 18 June 2019 à 07:20:12AM, Ray Luo a écrit : > > > Thomas, > > > > > > Sorry for the late reply. Somehow your emails are put into the SPAM > > > folder by gmail. > > > > > > The answer to your question is that in the newer releases, the inp=2 > > > option no longer considers radiopt, which is only related to inp=1. > > > > > > All the best, > > > Ray > > > -- > > > Ray Luo, Ph.D. > > > Professor of Structural Biology/Biochemistry/Biophysics, > > > Chemical Physics, Biomedical Engineering, and Chemical Engineering > > > Department of Molecular Biology and Biochemistry > > > University of California, Irvine, CA 92697-3900 > > > > > > On Tue, Jun 11, 2019 at 9:50 PM Thomas Gaillard > > > <thomas.gaillard.polytechnique.edu> wrote: > > > > > > > > Le Monday 13 May 2019 à 06:40:57PM, Thomas Gaillard a écrit : > > > > > Dear AMBER developers, > > > > > > > > > > Comparing MMPBSA results with radiopt option set to 0 or 1, I obtain > > > > > different values for the dispersion term (and of course for the PB term, > > > > > but the same value for the cavity term). Is this expected? > > > > > > > > > > This was already mentioned > > > > > (http://archive.ambermd.org/201702/0421.html). > > > > > > > > > > I was thinking that radiopt=1 would only affect the PB radii, not the > > > > > radii used for the cavity and dispersion terms. > > > > > > > > > > Thanks for your time, > > > > > > > > Hi, > > > > > > > > I am adding an example to illustrate my question. > > > > > > > > This is the PB test of MMPBSA.py > > > > (AmberTools/test/mmpbsa_py/02_Poisson_Boltzmann) with radiopt set to 0 > > > > or 1: > > > > > > > > MMPBSADI radiopt=0 > > > > &general > > > > startframe=1, endframe=2, interval=1, > > > > keep_files=0, debug_printlevel=2 > > > > / > > > > &pb > > > > istrng=0.1, inp=2, radiopt=[01], > > > > / > > > > > > > > Only the receptor energies are reported. > > > > > > > > radiopt=0: > > > > EPB -3255.0199 > > > > EDISPER -1134.8265 > > > > > > > > radiopt=1: > > > > EPB -3188.8747 > > > > EDISPER -1128.0331 > > > > > > > > Other terms (VDWAALS, EEL, ENPOLAR) are identical. > > > > > > > > I recall my question: is it expected that the EDISPER term is affected > > > > by radiopt? > > > > > > > > I can make other tests if it can help. > > > > > > > > Thanks, > > > > > > > > -- > > > > Thomas Gaillard > > > > Professeur assistant > > > > Laboratoire de Biochimie > > > > Ecole Polytechnique > > > > 91128 Palaiseau cedex > > > > tel: +33 1 69 33 48 62 > > > > fax: +33 1 69 33 49 09 > > > > thomas.gaillard.polytechnique.edu > > > > http://thomasgaillard.fr > > > > > > > > _______________________________________________ > > > > 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 > > > > -- > > Thomas Gaillard > > Professeur assistant > > Laboratoire de Biochimie > > Ecole Polytechnique > > 91128 Palaiseau cedex > > tel: +33 1 69 33 48 62 > > fax: +33 1 69 33 49 09 > > thomas.gaillard.polytechnique.edu > > http://thomasgaillard.fr _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jun 19 2019 - 14:30:03 PDT