AMBER Archive (2008)

Subject: AMBER: MM_PBSA binding error

From: Larry Layne (
Date: Thu Oct 30 2008 - 13:54:24 CDT

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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