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
