On Tue, Feb 19, 2013 at 9:31 AM, Saugata Hazra <saugata.iitk.gmail.com>wrote:
> 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.
>
Upgrading AmberTools is sufficient for MMPBSA.py.
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> *Know me Know fun, no me no fun!!!*
> Dr. Saugata Hazra
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 19 2013 - 07:00:03 PST
