Hi Shi,
Please follow the MMPBSA tutorial in AMBER
*(
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm
<
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm>*),
If you are, then you can see a DAT file as your final output the contains
DELTA G values. Moreover you can ask the script to create a log file, so
that you can monitor the progress of your run. The command to do the above
task would be
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y
*.mdcrd > process.log 2>&1
On Tue, Jan 12, 2016 at 3:40 AM, Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Hi,
>
> Are you certain that the job has finished running? It might still be
> writing to the disk- does the output or log file show that it's done? If it
> is, it might be an issue with the cluster itself so it might be worth
> asking whoever is in charge of it- I've had situations where my job was
> still shown to be 'running', even though nothing was actually being run.
>
> Best,
>
> Kenneth
>
> On Mon, Jan 11, 2016 at 2:29 PM, Guqin Shi <shi.293.osu.edu> wrote:
>
> > Hi all,
> >
> > I've been running mmpbsa job parallel on a super computer center.
> > Everything went well and apparently I've seen the Frames and Decomp dat
> > files are all written and finished (all the frames have been written).
> What
> > confuses me is that the job is still running when checking thru qstat.
> > However, I didn't find any files that is being updated. Of course, I can
> > manually kill the job but I am wondering what is behind... Anyway to
> check
> > it to see if there's something real running...?
> >
> > Thank you all!
> > Guqin
> >
> > --
> > Guqin SHI
> > The Ohio State University
> > College of Pharmacy
> > 500 W. 12th Ave.
> > Columbus, OH, 43210
> > (614)688-3531
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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--
Regards,
Pallavi Mohanty
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Received on Mon Jan 11 2016 - 21:00:03 PST
