AMBER Archive (2009)

Subject: RE: [AMBER] Error running MM script

From: Ray Luo (
Date: Mon May 18 2009 - 12:43:30 CDT


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 Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562

-----Original Message-----
From: [] On Behalf
Of Vikas Sharma
Sent: Monday, May 18, 2009 5:00 AM
To: amber
Subject: [AMBER] Error running MM 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: extract_coords.mmpbsa > extract_coords.log and binding_energy.mmpbsa > binding_energy.log

After i run binding_energy.mmpbsa > binding_energy.log i get
the following error

/opt/amber10/exe/sander -O
-i pbs -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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