On Tue, Dec 13, 2016 at 12:40 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hello,
>
> I used this general setting including definitions of
> ligand/receptor mask.
>
> -----------------------------------------
> MMPBSA.py input file for running GB
> &general
> interval=1,startframe=1
> keep_files=1, debug_printlevel=2
> ligand_mask=':641-722 | :1363-1444 '
>
Remove the trailing space between the last 4 and the '. The mask parser
in ParmEd should be fixed to strip leading and trailing whitespace.
> receptor_mask=:723-1362
> /
> --------------------------------------
>
> Unfortunately I obtained error:
>
> "MaskError: Illegal binary operation"
>
> Probably this refers to my ligand mask definition
> where operator "|" is used as logical AND to connect two groups
> of residues. This operator "|" works perfectly for example
> with pmemd, but in MMPBSA seems does not work.
>
| is the logical "or" operator.
& is the logical and operator. However, if you want residues 1-5 and
residues 11-15, you need to use "or". That selects all atoms belonging to
residues 1-5 *or* 11-15. Since no atom belongs to two residues, the
selection :641-722&:1363-1444 will select no atoms.
HTH,
Jason
--
Jason M. Swails
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Received on Tue Dec 13 2016 - 10:00:04 PST
