Hi Jason,
As wrote to Dan, the problem was using the 'CO' instead of 'C' for
carbonyl selection. I tried the parentheses, they work too and they
are probably more readable:
ACTION SETUP FOR PARM '../mut1_2w_noWATCl.prmtop' (2 actions):
0: [distance 4SGa :4.SG (:4.SG<:5.0)&.C out 4SGa.dist noimage]
:4.SG (1 atoms) to (:4.SG<:5.0)&.C (7 atoms), imaging off.
1: [distance 4SGb :4.SG .C&(:
4.SG<:5.0) out 4SGb.dist noimage]
:4.SG (1 atoms) to .C&(:
4.SG<:5.0) (7 atoms), imaging off.
Thanks a lot,
Krisztina
Quoting Jason Swails <jason.swails.gmail.com>:
> On Sat, Jul 5, 2014 at 7:18 AM, Krisztina Fehér <Krisztina.Feher.ugent.be>
> wrote:
>
>> Thanks for the shell script, Dan.
>>
>> One more question: can you combine a distance-based criterion with an
>> atom name selection? So, is it possible to select e.g. carbonyl atoms
>> within 5A distance from :4.SG? I tried to join these two selections
>> with "&":
>>
>> .C&:4.SG<:5.0
>>
>
> This is probably interpreted as (@C&:4.SG) < :5.0, which would not match
> anything.
>
>
>>
>> and
>>
>> :4.SG<:5.0&.C
>>
>> which did not work and would like to know why. Is there a limitation
>> in the use of the logical operators?
>>
>
> Maybe try parentheses:
>
> (:4.SG<:5.0)&.C or .C&(:4.SG<:5.0)
>
> You can increase the print level of mask evaluation (using the "prnlev"
> command, I think). This should show you the prefix and postfix notation
> that will more clearly represent how the mask is actually being evaluated
> if you continue to have troubles with masks.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Jul 05 2014 - 08:30:03 PDT
