[AMBER] Fwd: Creating a concatenated coordinate file for LES

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Sun, 29 Apr 2012 09:50:31 -0400

---------- 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
AMBER mailing list
Received on Sun Apr 29 2012 - 07:00:03 PDT
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