Re: AMBER: RED and Multi-Orientation

From: Raviprasad Aduri <>
Date: Tue, 06 Sep 2005 21:24:29 -0400

Dear Francois,
Thank you very much for the prompt reply. When do you think the RED III is
going to be available.
Raviprasad Aduri

At 03:35 AM 9/6/2005, you wrote:
>Quoting Raviprasad Aduri <>:
> > I am working on deriving partial charges for modified RNA bases. I am using
> > RED Ver.II to do the multi orientation fit.
>We found with Piotr that deriving RESP charges for RNA nuclosides/tides is
>really tricky, in particular for the sugar hydroxyls. Picking the good minimum
>is not that easy for RNA...
> > To my surprise the charge values are not consistent when I am going from
> > single orientation to 4,12 and 20 orientations in the case of Pseudouridine
> > with a methyl group replacing the sugar moiety ( methyl atoms are 10,11,12
> > and 13). When I used 1,4 and 12 orientations for N2-methyl Guanine (the
> > methyl group is 17,18,19 and 20) I see some consistency in their charge
> > values.
>A .05 charge difference (induced by a mol. orientation) is very common.
>I think we even found a max. diff. of .07 in one case (study based on more
>100 mol. orientations).
>Please see, this has been
>already discussed.
>It is why multi-orientation RESP/ESP fit has been implemented in R.E.D.
> > I am actually taking the resp inputs produced by the RED and putting the
> > Sugar charge constraint of 0.118186 (which I obtained when I did the resp
> > multi molecular fit for all the naturally occurring C3' endo nucleosides).
>0.1182, OK
>Yes, this part is now automatically handled in R.E.D.-III, we still have to
>write the manual & tutorials...
> > I am using the "espot" file produced by the RED as my esp input file.
> > I am attaching both the Pseudouridine and N2-methyl Guanine data in the
> > form of EXCEL sheets along with this mail.
> >
> > 1. I would like to know why Pseudouridine is behaving so differently when I
> > increase the number of orientations.
>I would 1st try to understand the charge orientation dependence using a simple
>molecule such as EtOH (very good example). And then in a 2nd step, see if this
>charge dependence is consistent with what you get with your new
> > 2. What is the minimum number of orientations we need to obtain reasonably
> > reproducible results for modified RNA bases.
>Reproducibility of RESP/ESP charges is achieved _because_ the molecular
>orientation of the minimum is fully known (controlled by the rigid-body
>reorientation algo.). Multi-orientation fit simply 'averages' the charge
>over several orientations.
>Once again see the FAQ-I
> > 3. Why do we equivalence the polar hydrogens in the first stage fitting and
> > the CH3 and CH2 in the second stage of fitting.
>This is the way developped by the Kollman's group in 1993-1995.
>Please see the R.E.D.-II manual page 18 and the corresponding publications.
>Regards, Francois
> • F.-Y. Dupradeau •
>DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
> ••••
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Received on Wed Sep 07 2005 - 02:53:00 PDT
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