Re: [AMBER] hbond analysis

From: Jason Swails <>
Date: Mon, 9 Sep 2013 08:15:21 -0400

On Sun, Sep 8, 2013 at 10:22 PM, Mary Varughese <>wrote:

> sir,
> is the command below ok for dna in explicit water?
> center :1-20 mass origin
> image origin center familiar
> center :1-38 mass origin //Na ions
> image origin center familiar
> center :1-5529 mass origin// water residue
> image origin center familiar

You can replace all of this with the single command:


What you have now seems like overkill, especially the last one. Before
autoimage, I would center the first molecule (or monomer, assuming you have
multiple, disconnected subunits), image everything around that first
monomer, then center and image again around the rest of the solute (the
solvent will take care of itself). In the case of DNA, unless it is some
sort of single-stranded loop, that means centering and imaging the first
strand, then centering and imaging both strands.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 09 2013 - 05:30:02 PDT
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