[AMBER] ambmask and periodic boundaries

From: Aseel Bala <balaahme.msu.edu>
Date: Thu, 20 Oct 2016 14:41:12 -0400

Hi all,

 

I am currently trying to use ambmask to identify all the molecules within a
certain distance (3 Angstroms) of a given molecule.

 

I have been using ambmask as follows:

ambmask -p simbox.prmtop -c frame3302.inpcrd -find ':3 <:3.0' > output.pdb

 

My problem is: when I ran the MD simulation to obtain the coordinates in
frame3302.inpcrd, I had periodic boundaries activated (constant pressure).

However when ambmask runs, it doesn't pick up images across a periodic
boundary that are within the distance I chose (in this case 3 angstrom. It
is only picking up the molecules within the original box that are within
that range.

 

Is there a way to get amber to find all molecules (original and image) that
are within 3 angstroms of the molecule I am interested in?

 

Any help will be very much appreciated!

 

Thanks,

--
 
Aseel Bala Ahmed
PhD Candidate, Chemical Engineering
Michigan State University
Office: Engineering Building Rm. 2246
Cell: 810-399-6212
 
 
 
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Received on Thu Oct 20 2016 - 12:00:02 PDT
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