below is the error msg i got
MMPBSA.py.MPI being run on 192 processors
ptraj found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/ptraj
sander found! Using
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/sander
Preparing trajectories with ptraj...
300 frames were read in and processed by ptraj for use in calculation.
Abort signaled by rank 0: [qb519:0] Got completion with error
IBV_WC_LOC_LEN_ERR, code=1, dest rank=8
Exit code -3 signaled from qb386
Killing remote processes...MPI process terminated unexpectedly
DONE
Regards,
Vani
On Sun, Apr 10, 2011 at 12:53 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Are you talking about the tutorial? The final results file can be
> downloaded in several locations on the tutorial site, it's not necessarily
> included in the zip files (I don't remember exactly where they are).
>
> If you're talking about no FINAL_RESULTS_MMPBSA.dat file appearing after
> you've run the sample calculation, we can't help without more information.
> The only reason it wouldn't print a final results file is if something went
> wrong, in which case we'd need the error message that was generated.
>
> All the best,
> Jason
>
> On Sun, Apr 10, 2011 at 9:55 AM, vani panguluri <vanipanguluri.gmail.com
> >wrote:
>
> > I got the MMPBSA files but i am not able to found the finalresults.dat
> file
> > in my output. can i know why it so happening.........
> >
> > Regards,
> > Vani
> >
> > On Fri, Apr 8, 2011 at 1:01 PM, Bill Miller III <brmilleriii.gmail.com
> > >wrote:
> >
> > > In this calculation, mmpbsa.in, 1err.solvated.prmtop, complex.prmtop,
> > > receptor.prmtop, ligand.prmtop and all files that end in .mdcrd are
> input
> > > files for this calculation. Everything except mmpbsa.in can be found
> in
> > > that
> > > zip file that I mentioned previously.
> > >
> > > -Bill
> > >
> > > On Fri, Apr 8, 2011 at 1:48 PM, vani panguluri <
> vanipanguluri.gmail.com
> > > >wrote:
> > >
> > > > in this the complex ,receptor and ligand are our input files or else
> we
> > > > need
> > > > to consider those files also from these Zip files.
> > > >
> > > > Regards,
> > > > Vani
> > > >
> > > > On Fri, Apr 8, 2011 at 12:15 PM, Bill Miller III <
> > brmilleriii.gmail.com
> > > > >wrote:
> > > >
> > > > > All of these files can be downloaded from Section 3.2 of the online
> > > > > tutorial
> > > > > (
> > > http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
> > > > ).
> > > > > All of the files necessary to run this MMPBSA.py calculation can be
> > > > > downloaded on that site as part of the tarball near the top of the
> > page
> > > > > called Est_Rec_top_mdcrd.tgz.
> > > > >
> > > > > I hope that helps.
> > > > >
> > > > > -Bill
> > > > >
> > > > > On Fri, Apr 8, 2011 at 1:01 PM, vani panguluri <
> > > vanipanguluri.gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Hello,
> > > > > >
> > > > > > In the MMPBSA.PY in protein- ligand complex how can I get the
> > > > > > *1err.solvated.prmtop
> > > > > > that *file i had done the prod steps as shown in the manual but i
> > got
> > > > > > stucked over this step
> > > > > > $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o
> > > FINAL_RESULTS_MMPBSA.dat
> > > > > -sp
> > > > > > 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> > > > > > ligand.prmtop -y *.mdcrd
> > > > > >
> > > > > > Can anyone explain me in detail about this step and how to get
> > those
> > > > > files
> > > > > >
> > > > > > Regards,
> > > > > > Vani
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Bill Miller III
> > > > > Quantum Theory Project,
> > > > > University of Florida
> > > > > Ph.D. Graduate Student
> > > > > 352-392-6715
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Bill Miller III
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-6715
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Apr 10 2011 - 11:30:03 PDT
