Re: [AMBER] files for RED

From: Urszula Uciechowska <>
Date: Thu, 25 Oct 2012 13:10:02 +0200

Dear Francois,

The RED runs are finished, for the sarin the calculations are complete I guess, attached is obtained conformation Mol_m1-o1-sm_sarin.mol2‎.
However for the cyklosarin an error occurred, attached is log and p2n files for the cyklosarin.
At the end of the cyklosarin file is:
Sum of Mulliken charges with hydrogens summed into heavy atoms = 0.00000
 Error termination request processed by link 9999.
 Error termination via Lnk1e in /usr/local/g09-userred/l9999.exe at Wed Oct 24 19:34:57 2012.
 Job cpu time: 1 days 8 hours 5 minutes 14.2 seconds.

 Do you know, what did go wrong? how can I avoid this error?

Thank you in advance
Urszula Uciechowska, Ph.D.
Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Von: FyD []
Gesendet: Mittwoch, 24. Oktober 2012 14:13
An: AMBER Mailing List
Betreff: Re: [AMBER] files for RED

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

AMBER mailing list

AMBER mailing list

Received on Thu Oct 25 2012 - 04:30:02 PDT
Custom Search