[AMBER] ambmask issue

From: Aseel Bala <balaahme.msu.edu>
Date: Thu, 17 Nov 2016 13:21:11 -0500

Hi everyone,
 I am trying to select all molecules within 3 angstroms of a residue(in this
case residue 16) using a mask.

I centered residue 16 in the middle of a 40x40x40 A box. Therefore I know
that there is plenty of space around it before I hit a boundary.

I have tried the syntax: qmmask='(:16 <:3.0)'

To select all residues within 3 A of residue 16 but to no avail. For some
reason, it tells me that the mask matches all the atoms in the box. It gives
me the same error when I choose even 1 A instead of 3.

Is there a problem with how I am writing the ambmask?

Thanks in advance,
Aseel Bala 
Michigan State University
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Received on Thu Nov 17 2016 - 10:30:02 PST
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