Thank you for the reply.
I tried running the decomposition with the serial version of MMPBSA.py but
again I got the same error.
#####################################33
Loading and checking parameter files for compatibility...
sander found! Using /apps/scratch/compile/amber18/bin/sander
cpptraj found! Using /apps/scratch/compile/amber18/bin/cpptraj
Preparing trajectories for simulation...
25001 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /apps/scratch/compile/amber18/bin/sander
calculating complex contribution...
bad atom type: i
File "/apps/scratch/compile/amber18/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File
"/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/apps/scratch/compile/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /apps/scratch/compile/amber18/bin/sander failed with prmtop
com_nowat.prmtop!
Exiting. All files have been retained.
#############################################
Can you please try to solve the error.
Why with the same *.prmtop and *.mdcrd GBSA and PBSA is running and getting
the results but showing error while running decomp?
Thanks
On Fri, Feb 5, 2021 at 7:18 PM David A Case <david.case.rutgers.edu> wrote:
> On Fri, Feb 05, 2021, Nisha Amarnath Jonniya wrote:
>
> >CalcError: /apps/scratch/compile/amber18/bin/sander failed with prmtop
> >com_nowat.prmtop!
> >Error occured on rank 2.
> >Exiting. All files have been retained.
>
> Please look at the mdout files for the sander run that used
> com_nowat.prmtop. Also, try a test run with the serial version of
> MMPBSA.py, to see if that helps, or maybe gives better error messages.
>
> ...dac
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Mon Feb 08 2021 - 21:30:02 PST
