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
Received on Fri Sep 20 2013 - 11:30:02 PDT
