---------- Forwarded message ----------
From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Thu, Apr 26, 2012 at 10:01 PM
Subject: Creating a concatenated coordinate file for LES
To: AMBER Mailing List <amber.ambermd.org>
Hello everyone,
I am trying to compare free energy changes along two intramolecular
tunnels in a protein, as an ammonia molecule passes through the tunnel from
one site to another site. I want to place copies of the ammonia molecule at
various points along the tunnel. Instead of running many simulations with
the ammonia molecule at different points along the tunnel I am trying to
use LES to place 6 copies of the ammonia molecule simultaneously at 6
positions along the tunnel. So the initial positions of the copies will be
different. In the chapter on LES in the Amber11 user manual it says I have
to concatenate different coordinates into a single file. So if I have an
initial .inpcrd file with one ammonia molecule could anyone give me the
specifics of creating the concatenated file?
Thank you
Sajeewa Dewage
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Received on Sun Apr 29 2012 - 07:00:03 PDT
