Thank you very much Jason.
One more question to make it sure.
As I have mentioned earlier, that I have Amber 11 & AmberTools 1.5.
So, is it enough to upgrade only the AmberTool or I also have to upgrade my
AMBER to AMBER12.
Thanks,
Saugata
On Tue, Feb 19, 2013 at 9:00 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Feb 19, 2013 at 8:02 AM, Saugata Hazra <saugata.iitk.gmail.com
> >wrote:
>
> > Hi,
> >
> > I am running a binding energy calculation (MM-PBSA) for protein-ligand
> > complex using Amber11 and AmberTools 1.5. I am following Ross Walker
> > tutorial but have got error message during MMPBSA calculation as follows:
> >
> > saugata.saugata:~/Desktop/ba2291/mdrun/ba2291_atp$ $AMBERHOME/bin/MMPBSA
> > -O
> > -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ba2291_atp_mg.prmtop -cp
> > ba2291_com.prmtop -rp ba2291_prot.prmtop -lp atp.prmtop -y *.mdcrd
> > Reading command-line arguments and input files...
> > Loading and checking parameter files for compatibility...
> > ptraj found! Using /home/saugata/amber11/bin/ptraj
> > mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
> > for GB calculations
> > mmpbsa_py_energy found! Using /home/saugata/amber11/bin/mmpbsa_py_energy
> > for PB calculations
> > Preparing trajectories for simulation...
> > 50 frames were read in and processed by ptraj for use in calculation.
> >
> > Beginning GB calculations with mmpbsa_py_energy...
> > calculating complex contribution...
> > calculating receptor contribution...
> > Segmentation fault (core dumped)
> >
>
> Yikes. A segfault from NAB. Try upgrading to AmberTools 12 and use that
> version instead. You can also try putting "use_sander=1" in the &general
> section of the MMPBSA.py input file to force it to use sander instead.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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>
--
*Know me Know fun, no me no fun!!!*
Dr. Saugata Hazra
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Received on Tue Feb 19 2013 - 07:00:02 PST
