On Sat, Apr 26, 2014 at 8:12 AM, James Starlight <jmsstarlight.gmail.com>wrote:
> Jason,
>
> one question. According to below log my GB calculations have been
> successfully finished but PB (with the same input files) result in the
> error during complex processing
>
>
> Beginning GB calculations with
> /home/own/Documents/simulations/amber/amber14/bin/sander
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
>
> Beginning PB calculations with
> /home/own/Documents/simulations/amber/amber14/bin/sander
> calculating complex contribution...
> File "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA.py", line
> 96, in <module>
> app.run_mmpbsa()
> File
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/main.py",
> line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/calculation.py",
> line 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/calculation.py",
> line 416, in run
> self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /home/own/Documents/simulations/amber/amber14/bin/sander failed
> with prmtop complex_dry22.prmtop!
>
>
>
> Exiting. All files have been retained.
>
> Why this should be and does it possible (1) look in some log file on the
> reason of such error
>
Look in _MMPBSA_complex_pb.mdout.0
> and (2) obtain results from the GB calculations only? (this time
> FINAL_RESULTS file have not been created).
>
You can run GB and PB calculations in separate calculations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 26 2014 - 05:30:04 PDT
