AMBER Archive (2006)

Subject: Re: AMBER: library for 8oxoguanine

From: FyD (fyd_at_u-picardie.fr)
Date: Tue Jul 25 2006 - 07:39:27 CDT

Quoting "Carra, Claudio (JSC-SK)[USRA]" <claudio.carra-1_at_nasa.gov>:

> i've been scrambling to make the correct library for the 8oxoGuanine
> in a sequence of base pairs, with a reasonably good orientation.
> i've already written to this forum for help on that but i didn't
> get any reply, so i'm simplifying my issue.
>
> I've followed the example proposed in the tutorial 4,
> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four_orig/
> but i got a problem with missing parameter for the force field,
> in generally fixable with parmchk, but not in this case since
> the residue is already inserted in the DNA chain.
>
> however the tutorial at the very and point out that
>
> [...]"Creating a set of parameters is a bit of an art, since one is
> often faced with unknown parameters (such as force constants for
> copper to its ligants as in this example). The purpose of this
> tutorial is simply to cover the mechanics of running AMBER and
> so I provide you all of the parameters below. Note, these are for
> tutorial purposes only, I make no claims about the validity or
> appropriateness of these parameters.[...]"
>
> so essentially my question is whether there is a TESTED way to
> produce a DNA chain, double and single strand, with a 8oxoguanine
> residue? the question can be extended to the general problem of
> changing one or more atom (for instance a carbossilic substituent
> with an amino group) on a given protein, and to make sure that
> is it properly bonded and describe by the force field, keeping
> a reasonably orientation from the starting guess.
>
> i would really appreciate any comment, even negative.

For deriving new nucleotides, you could look at the following R.E.DD.B.
(http://www.u-picardie.fr/labo/lbpd/REDDB/) projects:

F-59 2-(2'-Hydroxyphenyl)benzoxazole C-aryl-nucleotide fragment
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-59/
Corresponding RESP inputs:
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-59/input1.in
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-59/input2.in

F-58 2-(2'-Hydroxyphenyl)benzoxazole C-aryl-nucleotide fragment
F-57 (2R,3S)-3-Hydroxy-2-hydroxymethyl-tetrahydrofurane nucleotide fragment

Or the work of Jingyang Chen (different abasic sites):
Project F-64, F-63, F-62 & F61
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-64/

regards, Francois

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