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 - 04:30:03 PDT
