From: Jason Swails <>
Date: Fri, 20 Sep 2013 14:22:57 -0400

On Fri, Sep 20, 2013 at 6:41 AM, Jason Swails <>wrote:

> On Fri, Sep 20, 2013 at 1:25 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
>> 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 with the OP's input file, shown below, with the
previously-attached trajectory and topology file yields NaNs).


startframe=1, endframe=50, interval=1,

verbose=2, keep_files=1,


igb=5, saltcon=0.150,


istrng=0.15, fillratio=4.0

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 20 2013 - 11:30:02 PDT
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