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?
What else options for the mm-pbsa should be taken into account in case of
the dG of ligand- membrane proteins estimations?
James
2014-04-25 15:10 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Fri, 2014-04-25 at 11:27 +0400, James Starlight wrote:
> > Jason,
> >
> >
> > thanks for suggestions again.
> >
> >
> >
> > The addition of the box dims to the amber chamber have been resulted
> > in the same error.
> >
> > in _MMPBSA_complex_gb.mdout.0. I've found
> >
> --------------------------------------------------------------------------------
> > 3. ATOMIC COORDINATES AND VELOCITIES
> >
> --------------------------------------------------------------------------------
> >
> >
> > FATAL: NATOM mismatch in coord and topology files
>
> Ah, I think I know what's happening. By default, MMPBSA.py is supposed
> to strip all ions from the solvated topology file, but the atom names of
> the ions are set to the standard names that Amber uses. See the
> description of "strip_mask". You can also run
>
> MMPBSA.py --input-file-help # can be shortened to --input
>
> and you will get a listing of all variables you can specify in the input
> file along with their default. Try setting strip_mask to
>
> strip_mask=':WAT,CLA,POT'
>
> to make sure you get rid of the potassium and chloride ions.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri Apr 25 2014 - 07:30:03 PDT
