can you try to remove " " quote?
mask (:7.OP1<:4.0)&:Na+ maskout mask_A7OP1_Na.dat
Hai
On Thu, Aug 6, 2015 at 5:26 PM, Ucisik, Melek Nihan <ucisik.illinois.edu>
wrote:
> Hello,
> I am trying to count the number of sodium ions within 4 Å from a certain
> atom (OP1 of residue #7) and I composed the below mask command in analogy
> to the example given in the AmberTools manual:
>
> mask “(:7.OP1<:4.0)&:Na+” maskout mask_A7OP1_Na.dat
>
> The atom mask is not recognized by cpptraj and I get the following message:
>
> 0% Error: Could not parse mask [“(:7.OP1<:4.0)&:Na+”].
> Warning: Could not set up atom mask [“(:7.OP1<:4.0)&:Na+”]
> Warning: Action [mask “(:7.OP1<:4.0)&:Na+” maskout mask_A7OP1_Na.dat ]
> failed, frame 0.
>
> I tried several variations of the mask to see which part exactly is
> failing by eliminating the atom mask “@OP2”, increasing the distance to 20
> Å, and changing the second part to “&:A”, a much more common residue. None
> of these variations worked and I always got the same message. What am I
> doing wrong? (using CPPTRAJ V14.09 by the way)
>
> Thanks,
>
> M. Nihan Ucisik, PhD
> Department of Chemistry
> University of Illinois at Urbana-Champaign
> E-mail: ucisik.illinois.edu<mailto:ucisik.illinois.edu>
> Web: http://meleknihanucisik.weebly.com
>
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Received on Thu Aug 06 2015 - 17:30:02 PDT
