[AMBER] ambmask issue

From: Aseel Bala <balaahme.msu.edu>
Date: Mon, 16 Jan 2017 16:50:20 -0500

Hi everyone,

I still have not be able to find an answer to the question below. I am
thinking that this may be a bug in amber.

Now, I am interested in looking at the codes within sander that calculate
atom or residue selections through the ambmask.

Does anyone know which subroutine(s) within sander carries these operations
out so I know where to start looking?

 

Thanks,

 

--
 
Aseel Bala Ahmed
PhD Candidate, Chemical Engineering
Michigan State University
 
 
 
-----Original Message-----
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 Mon Jan 16 2017 - 14:00:02 PST