[AMBER] mask behavior with ions?

From: Kenneth Huang <khuang8.student.gsu.edu>
Date: Wed, 18 Jul 2018 17:37:01 +0000

Hi all,

I'm seeing some odd behavior with mask when searching for ions around a residue- specifically, when I try to search for Na+ ions around one residue with the command

   mask "(:11.CD<:5.5)&:Na+" maskout maskout_E11-Na+.dat

The output looks like it's searching for Na+ to Na+ instead of the specified residue to Na+?

#Frame AtomNum Atom ResNum Res MolNum
       8 3269 Na+ 210 Na+ 63
      17 3243 Na+ 184 Na+ 37
      18 3243 Na+ 184 Na+ 37
      19 3243 Na+ 184 Na+ 37
      35 3223 Na+ 164 Na+ 17

Trying a variation of the command by just picking up on anything that isn't protein within a 5.5 radius-

    mask "(:11.CD<:5.5)&!:1-104" maskout maskout_E11-Na+.dat

Seems to reproduce the exact same results, so I'm not sure if it's actually working as intended, or a bug?


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Received on Wed Jul 18 2018 - 11:00:02 PDT
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