Re: [AMBER] files for RED

From: FyD <>
Date: Wed, 24 Oct 2012 14:13:03 +0200

Dear Urszula,

> 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.

Chemical equivalencing is correct this time.

You use a single INTRA-MCC for the 2 capping groups; strictly, this is
correct, but this is not the 'Amber' approach, where an intra-mcc set
to zero is used for each capping group.

Do you agree with the conformation you generated? is it in agreement
with experimental data? and/or is it the lowest minimum? an
alternative could be to split this whole molecule into two building

regards, Francois

> 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;
> See
> 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 - 05:30:03 PDT
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