RE: AMBER: MM_PBSA binding error

From: Larry Layne <>
Date: Fri, 31 Oct 2008 08:56:42 -0400 (EDT)


I checked my out file for that ligand and sure enough, there is an error.
It reads:

PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000.

I've attached the output file. I'm not sure what that means or how to remedy the problem. Is it saying the grid I am suing to do the PBSA calculation is too large? Any suggestions would be helpful.


> Dear Larry,
> I just tested your files with the following input file from amber9 test
> cases:
> test of PB reaction field on protein g solvated in a sphere &cntrl ntx=1,
> irest=0, imin=1, ntmin=2, maxcyc=0, ntpr=1, igb=10, ntb=0, ntc=1, ntf=1,
> tol=0.000001, / &pb npbverb=1, istrng=0, epsout=80.0, epsin=1.0, space=.5,
> accept=0.001, sprob=1.6, radiopt=1 /
> And I was able to run it. You may want to take a look of the sander/pbsa
> output file if it's still in the directory ... Is there any error
> messages inside?
> All the best, Ray
> ========================================== 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 Web:
> ==========================================
> -----Original Message----- From:
> [] On Behalf Of Larry Layne Sent: Thursday,
> October 30, 2008 11:54 AM To: Subject: AMBER: MM_PBSA
> binding error
> I am having some trouble with running MM_PBSA. I can generate the
> snapshots that I need, but sander has trouble during the calculation and
> reports an error as follows:
> /usr/local/amber9/exe/pbsa -O -i -o pbsa_lig.5.out -c
> ./snapshot_lig.crd.5 -p ../../pdz1/ligand/DSLA.prmtop not successful.
> I am trying to perform an alanine scan on a tetra-peptide ligand and have
> gotten the error for the above error for the native ligand and the first
> alanine replacement. If I bypass the snapshot_lig.crd.39 file for the
> native ligand, by removing it from the directory, mm_pbsa continues to
> snapshot_lig.crd.40 without error and produces an output file with a
> reasonable value. I moved to the first alanine mutation to see if the
> problem continued and it does.
> I would appreciate any help fixing this problem. I've attached the
> following files:
> snapshot_lig.crd.5 - the problem file listed above DSLA.prmtop - the
> associated topology file binding_energy.mmpbsa - the input for binding
> energy calculation binding_energy.log - the associated log
> extract_coords.mmpbsa - the input for the creation of snapshots from my
> trajectory file extract_coords.log - the associated log
> Thanks for your help, Larry

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Received on Sun Nov 02 2008 - 05:07:21 PST
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