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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Wed, Sep 25, 2013 at 6:41 PM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <sumra.msbi30.iiu.edu.pk> wrote: > Dear Ray > you mean to say in my prmtop there is no single charge?? > if yes then when i tried to add charge in ligand it was promoted that no > charge required > > Regards > > > > Sumra Wajid Abbasi > PhD Scholar > Computational Biology Lab, National Center for Bioinformatics > Quaid-e-Azam University, Islamabad-45320 Pakistan. > > > On Thu, Sep 26, 2013 at 2:45 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: > >> Okay, we can also reproduce the NaN issue. It turns out that there is >> not a single charge in the prmtop file. They are all zero! >> >> Ray >> -- >> Ray Luo, Ph.D. >> Professor, >> Biochemistry, Molecular Biophysics, and >> Biomedical Engineering >> University of California, Irvine, CA 92697-3900 >> >> >> On Fri, Sep 20, 2013 at 11:22 AM, Jason Swails <jason.swails.gmail.com> >> wrote: >> > On Fri, Sep 20, 2013 at 6:41 AM, Jason Swails <jason.swails.gmail.com >> >wrote: >> > >> >> >> >> >> >> >> >> On Fri, Sep 20, 2013 at 1:25 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 < >> >> sumra.msbi30.iiu.edu.pk> wrote: >> >> >> >>> Dear Smith >> >>> >> >>> Yeah you are right i loaded the ligand into VMD using Coordinates With >> >>> Periodic Box info. now i load without Periodic Box info and image looks >> >>> fine..But still calculation issue is there.. >> >>> >> >> >> >> Upgrade to AmberTools 13 and see if the issue persists. If the problem >> is >> >> fixed under the latest (free) version, it is unlikely to be fixed in >> older >> >> (unsupported) versions. >> >> >> > >> > I can verify that the current PB code generates NaN results for the polar >> > solvation with your snapshots. Hopefully a PBSA developer can take a >> look >> > at it (running MMPBSA.py with the OP's input file, shown below, with the >> > previously-attached trajectory and topology file yields NaNs). >> > >> > &general >> > >> > startframe=1, endframe=50, interval=1, >> > >> > verbose=2, keep_files=1, >> > >> > / >> > &gb >> > >> > igb=5, saltcon=0.150, >> > >> > / >> > &pb >> > >> > istrng=0.15, fillratio=4.0 >> > / >> > >> > >> > All the best, >> > 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/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 Wed Sep 25 2013 - 20:30:03 PDT