Thanks Jason, it helped !
Sorry for the confusion of the logic operators.
Best wishes,
Marek
Dne Tue, 13 Dec 2016 18:47:29 +0100 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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
>
--
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Received on Tue Dec 13 2016 - 13:30:02 PST
