On Sat, Apr 26, 2014 at 8:35 AM, James Starlight <jmsstarlight.gmail.com>wrote:
> 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) ?
>
No -- if you google "PB Bomb in pb_aaradi" it should bring you to some
threads with suggested solutions.
>
> 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 ?
>
You can look at using the quasi-harmonic approximation to approximate
vibrational modes. It requires a long simulation to converge, though.
(Alternatively, you can minimize a handful of structures and run very low
temperature MD (~20-50K) to get results that are almost indistinguishable
from normal mode analysis, but this is rather uncommon and would need to be
done by hand since MMPBSA.py doesn't automate this procedure).
> 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).
>
The tutorial has a section about running in parallel -- it's similar to
running sander or pmemd in parallel (i.e., it is an MPI-parallelized
program). See
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section4.htm
HTH,
Jason
>
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 26 2014 - 06:00:03 PDT
