AMBER Archive (2006)

Subject: Re: AMBER: library for 8oxoguanine

From: Carlos Simmerling (
Date: Mon Jul 24 2006 - 16:12:38 CDT

we've done 8-oxo-G simulations with Amber and have
a frcmod file that we can share if you're interested. Contact me
directly if you want it. You might also check our article

Cheng, X., Kelso, C., Hornak, V., de los Santos, C., Grollman, A. and
Simmerling, C., /“Dynamic Behavior of DNA Base Pairs Containing
8-oxoguanine”/, J. Am. Chem. Soc., 127:13906, 2005

we also have another article on 8OG in press in Biochemistry.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University E-mail:
Stony Brook, NY 11794-5115

Academic year 2005 address:
Brookhaven National Laboratory
Computational Science Center
Upton, NY 11973

M. L. Dodson wrote:

>On Monday 24 July 2006 14:50, Carra, Claudio (JSC-SK)[USRA] wrote:
>>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
>Maybe I am misunderstanding you, but you do not modify the
>original DNA to produce a new DNA with an 8OG residue. Instead,
>you generate a new residue, 8OG, complete with all the charges,
>topology, etc similar to what the regular DNA residues have. You
>may need to generate a frcmod file that contains additions to the
>force field if your new residue contains bonds, angles or torsions
>that are not present in the regular force field description.
>I suggest you use Antechamber or REDII (see the archives for many
>references to the location of REDII). The Antechamber web page
>gives examples of generating residue descriptor files for new
>residues. REDII automates the procedure, but is somewhat oriented
>toward standalone chemical compounds. Since you are generating a
>polymer internal residue, you will need to become pretty familiar
>with the resp software to use REDII. It may be that the new
>database section for the REDII web site has tutorials to do what
>you want.
>Once you have the new 8OG residue description, you can build your
>DNA using it for MD.

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