AMBER Archive (2005)

Subject: AMBER: RED and Multi-Orientation

From: Raviprasad Aduri (rpaduri_at_chem.wayne.edu)
Date: Mon Sep 05 2005 - 21:34:56 CDT

Dear Francois,
I am working on deriving partial charges for modified RNA bases. I am using
RED Ver.II to do the multi orientation fit.
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.
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).
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.
2. What is the minimum number of orientations we need to obtain reasonably
reproducible results for modified RNA bases.
3. Why do we equivalence the polar hydrogens in the first stage fitting and
the CH3 and CH2 in the second stage of fitting.

I will be greatly indebted for your precious time.

Thanking you
Sincerely
Raviprasad Aduri


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