Jason,
in this log I've found:
PB Bomb in pb_aaradi(): No radius assigned for atom 1 N NH3
Will it be fixed if my prmtop files for complex receptor and ligand will be
created with the assigned radii (e.g using --radii=mbondi2 flag) ?
2)Also I've found that NM calculations are not possible with the CHAMBER
generated prmtops using options from the tutorial. Are the any other
possibilities to calculate vibrational entropy terms for such cases ?
3)Finally what should I provide to the input to use all available CPU cores
of my workstation ? (with the default settings only 1 core from 4 available
on my i5 CPU have been used).
James
2014-04-26 16:26 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> 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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>
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Received on Sat Apr 26 2014 - 06:00:02 PDT
