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: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Larry Layne
Sent: Thursday, October 30, 2008 11:54 AM
To: amber.scripps.edu
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 pbsa.in -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 Fri Oct 31 2008 - 05:11:44 PDT
