AMBER Archive (2009)

Subject: Re: [AMBER] Error running MM script

From: Vikas Sharma (
Date: Tue May 19 2009 - 10:02:21 CDT

Dear Dr. Ray Luo,
Thanks for the reply..
i have pasted the file at end of this mail...
i had the same error and one of the users told me to add "fillratio = 4.0" to my binding_energy.mmpbsa ...i did that and again i got the same error...

how can i resolve this error?



  NB-update: residue-based nb list 654
  NB-update: atom-based nb list 773

======== Setting up Grid Parameters
Using bounding box for grid setup
Bounding Box Center: 26.500 52.000 29.500
Xmin, Xmax, Xmax-Xmin: 21.866 30.793 8.927
Ymin, Ymax, Ymax-Ymin: 45.236 58.330 13.094
Zmin, Zmax, Zmax-Zmin: 22.565 36.388 13.823
   beginning box center at level 1 26.500 52.000 29.500
   beginning box center at level 2 26.500 52.000 29.500
Grid dimension at level 1 5 9 9
Grid origin corrected at level 1 14.500 32.000 9.500
Grid dimension at level 2 33 41 43
Grid origin corrected at level 2 18.000 41.500 18.500
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000

From: Ray Luo <>
To: AMBER Mailing List <>
Sent: Monday, 18 May, 2009 11:13:30 PM
Subject: RE: [AMBER] Error running MM script


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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