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 and (2) obtain results from the GB calculations only?
(this time FINAL_RESULTS file have not been created).
James
2014-04-25 19:10 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Fri, 2014-04-25 at 18:17 +0400, James Starlight wrote:
> > Jason,
> >
> > many thanks!
> >
> >
> >
> > the addition of the
> >
> > &general
> > endframe=150, keep_files=2, strip_mask=':WAT,CLA,POT,POPE,POPC'
> >
> >
> > have been solved problem.
> >
> >
> > In the manual I've found that using gb=2
> > " PBradii mbondi2" to prepare the prmtop file should be set.
> >
> > Does some modification of the --radii=RADIUS_SET variable or some
> > other radius definitions are needed for such calculations?
>
> Yes, when running ante-MMPBSA.py you should use "--radii=mbondi2" to
> generate the mbondi2 radii for your system.
>
> Alternatively, you can use the "changeRadii mbondi2" command in ParmEd
> to do this to the topology files you already have. (ante-MMPBSA.py
> actually uses ParmEd behind-the-scenes).
> >
> >
> > What else options for the mm-pbsa should be taken into account in case
> > of the dG of ligand- membrane proteins estimations?
>
> You should go through the options in the manual, and maybe
> cross-reference the options there with what you have seen people use in
> other (related) studies.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 26 2014 - 05:30:03 PDT
