Re: [AMBER] MMPBSA/GBSA error

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 25 Sep 2013 20:25:41 -0700

Yes, not a single atom has partial charge. All charges are identically
ZERO in the prmtop file.

You have to rerun antechamber to get the prmtop right ... The program
should get charges etc set up for you automatically. I don't
understand what you mean by saying "when i tried to add charge in
ligand it was promoted that no charge required". How did you add
charge in the first place?

Ray
--
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
>> > _______________________________________________
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>> > AMBER.ambermd.org
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>>
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Received on Wed Sep 25 2013 - 20:30:03 PDT
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