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
>
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Received on Wed Sep 25 2013 - 19:00:02 PDT
