Re: [AMBER] MMPBSA/GBSA error

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 20 Sep 2013 14:22:57 -0400

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 - 11:30:02 PDT
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