Take a look in the other files. Perhaps the STDOUT and STDERR files have
some errors written in them? Or the _MMPBSA_*.mdout files have something
written in them? Take a look at the other files written my MMPBSA.py.
-Bill
On Fri, Oct 1, 2010 at 5:51 AM, Mannan <malie_03.yahoo.co.in> wrote:
>
> Hi,
> I am using Amber11 for the MMPBSA.py
> I have Bromine atoms in this set up, So I ran the MMPBSA.py in amber11
>
> To my surprise the job went without any error, but produced no results in
> the output.
> | Run on Fri Oct 1 17:28:56 SGT 2010
>
> |Input file:
> |--------------------------------------------------------------
> |Input file for running PB and GB in serial
> |&general
> | endframe=50, keep_files=2,
> |/
> |&gb
> | igb=2, saltcon=0.100,
> |/
> |&pb
> | istrng=0.100,
> |/
> |
> |--------------------------------------------------------------
> |Solvated complex topology file: BS2-tip3p.top
> |Complex topology file: BS2.top
> |Receptor topology file: SR.top
> |Ligand topology file: BS.top
> |Initial mdcrd(s): BS2-tns.mdcrd
> |
> |Best guess for receptor mask: ":1-262"
> |Best guess for ligand mask: ":263"
> |Ligand residue name is "UNK"
> |
> |Calculations performed using 50 frames.
> |Poisson Boltzmann calculations performed using internal PBSA solver in
> sander.
> |
> |All units are reported in kcal/mole.
>
> How can I over come this issue,
>
> Thanks,
> Mannan
>
>
> --- On Fri, 1/10/10, Giorgos Lamprinidis <lamprinidis.pharm.uoa.gr> wrote:
>
> From: Giorgos Lamprinidis <lamprinidis.pharm.uoa.gr>
> Subject: [AMBER] runing mmpbsa.pl on cluster
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Friday, 1 October, 2010, 2:28 PM
>
> 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
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>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Oct 01 2010 - 04:00:06 PDT
