Hi,
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>
app.run_mmpbsa()
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
self.prmtop))
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
