[AMBER] MMPBSA.py decomp, -deo, PB only problem

From: Ryan Pavlovicz <pavlovicz.7.osu.edu>
Date: Fri, 26 Jul 2013 11:29:34 -0400


I am experiencing a problem using the MMPBSA.py.MPI script when it comes to
calculating the DELTA energies for every frame of a decomposition (-deo)
when only PB calculations are called for.

Here is my input file:

  endframe=4000, verbose=2, keep_files=2,
  istrng=0.150, inp=1, cavity_offset=0.92, cavity_surften=0.00542,
  idecomp=1, print_res="1-255"

And the output:

Loading and checking parameter files for compatibility...
sander found! Using /usr/local/amber/amber12/bin/sander
cpptraj found! Using /usr/local/amber/amber12/bin/cpptraj
Preparing trajectories for simulation...
4000 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning PB calculations with /usr/local/amber/amber12/bin/sander
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...
UnboundLocalError: local variable 'gb_com' referenced before assignment
Error occured on rank 0.
Exiting. All files have been retained.
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

This only occurs when I don't include the GB calculations. The -deo output
will print the PB complex, receptor, and ligand info, but fails when it
gets to the 'DELTAS:' section.

I am experiencing this problem with the AmberTools version 13.13.

This seems like a possible bug, so i thought i'd bring it to someone's


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Received on Fri Jul 26 2013 - 09:00:04 PDT
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