AMBER Archive (2008)

Subject: RE: AMBER: MM_PBSA binding error

From: Ray Luo (
Date: Thu Oct 30 2008 - 14:35:36 CDT

Dear Larry,

I just tested your files with the following input file from amber9 test

test of PB reaction field on protein g solvated in a sphere
   ntx=1, irest=0,
   imin=1, ntmin=2, maxcyc=0,
   ntpr=1, igb=10, ntb=0,
   ntc=1, ntf=1, tol=0.000001,
   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

All the best,

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
Larry Layne
Sent: Thursday, October 30, 2008 11:54 AM
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,

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