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 - 05:11:31 PDT
