Vikas,
Can you take a lot of your pbsa_lig.8.out? There should be an error message
inside before the premature termination of the program.
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of Vikas Sharma
Sent: Monday, May 18, 2009 5:00 AM
To: amber
Subject: [AMBER] Error running MM _PBSA.pl script
Dear All,
I am using AMBER10... I am using MM PBSA for calculating Binding free energy
of a ligand...
i ran 1 ns production MD..
i used the following commands:
mm_pbsa.pl extract_coords.mmpbsa > extract_coords.log and
mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
After i run mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log i get
the following error
/opt/amber10/exe/sander -O
-i pbs a_lig.in -o pbsa_lig.8.out -c
/home/bharatam/amberresults1/vikamb_q1results/snap shot_lig.crd.8 -p
/home/bharatam/amberresults1/vikamb_q1/mol.prmtop not successful
mol is the name of my ligand...
How can i overcome this error?????
Please help...
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Received on Wed May 20 2009 - 17:21:34 PDT
