Wes is looking into this ...
Ray
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 Fri Sep 20 2013 - 12:30:02 PDT
