Re: [AMBER] files for RED

From: FyD <>
Date: Mon, 22 Oct 2012 17:44:09 +0200

Dear Urszula,

> I prepared two p2n files for RED server ( sarin and cykosarin).
> However I am not quite sure if they are correct or I need to add
> something else.

You used Ante_R.E.D. 1.x to generate these P2N files; please use
instead R.E.D. Server/Ante_R.E.D. 2.0 because Ante_R.E.D. 1.x does not
handle chemical equivalencing between different chemical groups;

For Sarin, the two terminal methyl groups in the side chain should be
equivalenced; i.e. they should bear both the following names: CT16 H16
H16 H16 or both CT17 H17 H17 H17

For cyclosarin, same type of remarks for the methylene group in the
pseudo cyclohexane group: CT15 and CT19 should bear the same number;
same remark for CT16 and CT18.
You have two additional hydrogen atoms in this dipeptide; I am not
sure this is correct...

then, I would check that the optimized geometry for each of these
dipeptides corresponds to what I want after geometry optimization.

finally, is your P atom asymmetric?

regards, Francois

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Received on Mon Oct 22 2012 - 09:00:02 PDT
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