Re: AMBER: RED and Multi-Orientation

From: FyD <>
Date: Tue, 06 Sep 2005 09:35:58 +0200

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 than
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 values
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 Tue Sep 06 2005 - 08:53:01 PDT
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