On Fri, Oct 1, 2010 at 7:46 AM, Giorgos Lamprinidis <
lamprinidis.pharm.uoa.gr> wrote:
> Jason,
>
> Thanks for your detailed response. However there is no sanmin_com1.in or
> out
> file. Here is the full error message from pbs
> /users/health/emikros/NMODE: Permission denied.
> /users/health/emikros/amber10//exe/sander -O -i sanmin_com.in -o
> sanmin_com.1.out -c /users/health/emikros/NMODE/snapshot_com.crd.1 -p
> /users/health/emikros/NMODE/era_ago_gen_com.prmtop -r sanmin_com.1.restrt
> not running properly
> My working direcory is /users/health/emikros/NMODE and the directory for
> sander is /users/health/emikros/amber10//exe/sander
> but for some reason the perl script can't write the input file.
>
Check your permissions here. MMPBSA.py operates mainly by relative paths,
so you may have less of a problem using this version. However, this seems
like a relatively simple issue to fix for the perl script.
Good luck!
Jason
> I shall also try to run the python version of mmpbsa.....
>
> George
>
>
>
>
> ----- Original Message -----
> From: "Jason Swails" <jason.swails.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Friday, October 01, 2010 1:37 PM
> Subject: Re: [AMBER] runing mmpbsa.pl on cluster
>
>
> > Hello,
> >
> > What is the error reported in sanmin_com.1.out? mm_pbsa.pl creates
> these
> > input and output files, so it can just create them in the current working
> > directory and not use any PATH prefix. I don't think this is your error.
> > Check sanmin_com.1.out for the relevant error message. Also, you may
> > consider checking out MMPBSA.py at
> > ambermd.org/tutorials/advanced/tutorial3/py_script. It has an MPI
> option
> > (though there are prerequisites installations to do before it can be
> > used).
> >
> > To use sander.MPI in the mm_pbsa.pl script, you'll have to find out
> where
> > sander is called (grep will certainly help here), and substitute in
> > something like "mpirun -np # sander.MPI" or something. Note that this
> may
> > struggle with some MPI implementations... Also, this will have no
> > (positive) effect on PB calculations, and it won't parallelize the actual
> > Hessian diagonalization for nmode. The version of mm_pbsa.pl included
> > with
> > amber11 spawns new compute threads to complete tasks, and MMPBSA.py has
> an
> > MPI version that can be used to split the calculation up across several
> > frames.
> >
> > Hope this helps,
> > Jason
> >
> > On Fri, Oct 1, 2010 at 4:58 AM, Giorgos Lamprinidis <
> > lamprinidis.pharm.uoa.gr> wrote:
> >
> >> Dear amber users,
> >>
> >> I am using AMBER 10.
> >> I am trying to run mmpbsa.pl script on a cluster machine using MPI.
> >> When i run my PBS file i get the following error:
> >> /users/health/emikros/amber10//exe/sander -O -i sanmin_com.in -o
> >> sanmin_com.1.out -c /users/health/emikros/NMODE/snapshot_com.crd.1 -p
> >> /users/health/emikros/NMODE/era_ago_gen_com.prmtop -r
> sanmin_com.1.restrt
> >> not running properly
> >>
> >> As you can see i need to give the EXACT path for all files when runing
> >> sander. The prmtop and crd files have the correct path because i defined
> >> them on binding_energy.mmpbsa script.
> >> So, how can i define the exact path for all input and output files?
> >> Also how can i define to use sander.MPI instead of sander?
> >>
> >>
> >> Thanks for your time,
> >> Dr. George Lamprinidis
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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. Graduate Student
352-392-4032
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Received on Fri Oct 01 2010 - 05:30:08 PDT
