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

From: Carlos Simmerling <>
Date: Mon, 30 Apr 2012 12:24:33 -0400

when you only replicate a few atoms, the easiest way is probably to create
a pdb file and duplicate those lines.

On Thu, Apr 26, 2012 at 10:01 PM, Sajeewa Pemasinghe <>wrote:

> 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 Mon Apr 30 2012 - 09:30:04 PDT
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