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
_______________________________________________
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
Received on Fri Oct 01 2010 - 03:00:03 PDT
