[AMBER] MMPBSA.py CalcError on ligand contribution only

From: Leandro Bortot <leandro.obt.gmail.com>
Date: Thu, 25 Aug 2016 11:43:11 -0300

Dear users,

     I searched the list and couldn't find an answer to this problem.
Related errors were on the MPI version while I use the serial version.
     I'm trying to run a MMPBSA calculation in which MMPBSA.py gives an
error only when calculating the ligand contribution. This doesn't make
sense to me since the complex contribution is calculated normally and all
prmtops were created together in tleap.
     Do you have any suggestions about how to solve this? The output is

Loading and checking parameter files for compatibility...
sander found! Using /path_to_amber16/bin/sander
cpptraj found! Using /path_to_amber16/bin/cpptraj
Preparing trajectories for simulation...
1 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning PB calculations with /path_to_amber16/bin/sander
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...
  File "/path_to_amber16/bin/MMPBSA.py", line 100, in <module>
  File "/path_to_amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
line 431, in run
    self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /path_to_amber16/bin/sander failed with prmtop lig.0.prmtop!

Exiting. All files have been retained.

Best regards,
AMBER mailing list
Received on Thu Aug 25 2016 - 08:00:02 PDT
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