Re: [AMBER] MMPBSA/GBSA error

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 25 Sep 2013 14:45:35 -0700

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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Received on Wed Sep 25 2013 - 15:00:02 PDT
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