Re: [AMBER] files for RED

From: Urszula Uciechowska <>
Date: Wed, 24 Oct 2012 12:23:44 +0200

Dear Francois,

I run RED 2.0 I hope that the p2n file are ok now. Could you please have a look at them?
The additional H were removed, and the P atom is asymmetric that is correct. The conformations of the
sarin and cyklosarin were taken from the xray structures.

best regards
Von: FyD []
Gesendet: Montag, 22. Oktober 2012 17:44
An: AMBER Mailing List
Betreff: Re: [AMBER] files for RED

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 Wed Oct 24 2012 - 03:30:02 PDT
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