Re: [AMBER] files for RED

From: Urszula Uciechowska <>
Date: Sat, 27 Oct 2012 16:30:06 +0200

Dear Francois,

I obtained the geometry from the RED server. Now I was wondering if I should use the amber99 atom types like MOL_p1.mol2 or
apply gaff and use the MOL.mol2? Anyway in both cases I am getting some errors about missing parameters.
Could you please suggest me how to correct them? and which option should I use?

best regards

Von: FyD []
Gesendet: Donnerstag, 25. Oktober 2012 14:34
An: AMBER Mailing List
Betreff: Re: [AMBER] files for RED


> The RED runs are finished, for the sarin the calculations are
> complete I guess, attached is obtained conformation
> Mol_m1-o1-sm_sarin.mol2?.

Seems ok to me; see the attached image...

And using LEaP I get:

Welcome to LEaP!
(no leaprc in search path)
> X = loadmol2 Mol_m1-o1-sm_sarin.mol2
Loading Mol2 file: ./Mol_m1-o1-sm_sarin.mol2
Reading MOLECULE named MOL
> charge X
Total unperturbed charge: -0.000000
Total perturbed charge: -0.000000

> 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?

The R.E.D. log reports:

  Geometry optimization(s) is/are being computed for molecule 1 ... [ FAILED ]
        See the file(s) "JOB1-gau_m1-1.out"

        Geometry optimization convergence problem
        Re-run the job using the best geometry obtained

I think the structure did not converge in the Gaussian geometry
optimization; you have to select the best (or the last) "Standard
orientation" from the Gaussian log file; and copy the corresponding
Cartesian coordinates in the P2N file and re-run R.E.D.; the format of
the X, Y and Z columns in the P2N file does have to be strictly that
of the PDB file format; thus you can do a crude copy/cut of these
cart. coordinates taken from the Gaussian log into the P2N file...

regards, Francois

> 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
> blocks.
> 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 Sat Oct 27 2012 - 08:00:03 PDT
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