Re: [AMBER] pdb file with a covalently linked nerve agent

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 28 Nov 2011 13:04:32 -0500

On Mon, Nov 28, 2011, Urszula Uciechowska wrote:
>
> In my pdb file I have covalently linked nerve to serine203, (attached
> pdb file). I was wondering if anyone could suggest me how to get
> the parameters for this residue, would be enough to use antechamber
> somehow?

Antechamber can work with modified amino acid residues, see the second item at
http://ambermd.org/antechamber/example.html; remember that you need to add all
hydrogen atoms first.

Another option is R.E.D.: see the links from the Amber web page. R.E.D. would
be my preference, for reasons that you can see on its web page.

...good luck....dac


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Received on Mon Nov 28 2011 - 10:30:03 PST
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