AMBER Archive (2009)

Subject: Re: [AMBER] Error running MM _PBSA.pl script

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Mon May 18 2009 - 23:34:18 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?

thanks

  4. RESULTS
--------------------------------------------------------------------------------

  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 <ray.luo_at_uci.edu>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Monday, 18 May, 2009 11:13:30 PM
Subject: RE: [AMBER] Error running MM _PBSA.pl script

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_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_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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