[AMBER] "mask" command failure

From: Ucisik, Melek Nihan <ucisik.illinois.edu>
Date: Thu, 6 Aug 2015 21:26:40 +0000

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)


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 - 14:30:03 PDT
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