From: RITUPARNA ROY <ritup176122023.iitg.ac.in>
Date: Sat, 30 Nov 2019 16:48:26 +0000


I am trying to run MMGBSA per residue and encountered the following error:

Loading and checking parameter files for compatibility...
sander found! Using /home/saikat/software/amber18/bin/sander
cpptraj found! Using /home/saikat/software/amber18/bin/cpptraj
Preparing trajectories for simulation...
51 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /home/saikat/software/amber18/bin/sander
  calculating complex contribution...
 bad atom type: O3
  File "/home/saikat/software/amber18/bin/MMPBSA.py", line 100, in <module>
  File "/home/saikat/software/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/saikat/software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/saikat/software/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run
CalcError: /home/saikat/software/amber18/bin/sander failed with prmtop peptide-atp.prmtop!
Exiting. All files have been retained.
Cleaning temporary files and quitting.

However, without the &decomp namelist, there was no error. Kindly help.

Rituparna Roy,

Junior Research Fellow,

Department of Chemistry,

Indian Institute of Technology Guwahati.
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Received on Sat Nov 30 2019 - 09:00:01 PST
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