AMBER: library for 8oxoguanine

From: Carra, Claudio \(JSC-SK\)[USRA] <"Carra,>
Date: Mon, 24 Jul 2006 14:50:59 -0500

Dear All,
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,
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.
thanks a lot
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Received on Wed Jul 26 2006 - 06:07:08 PDT
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