Re: AMBER: peptide-DNA crosslink modeling

From: M. L. Dodson <>
Date: Fri, 02 Jul 2004 13:06:39 -0500

On Friday 02 July 2004 12:01 am, David A. Case wrote:
> On Thu, Jul 01, 2004, M. L. Dodson wrote:
> >
> > I need to model a 4aa peptide crosslinked to DNA (N2-guanine) via
> > a propano group. I have generated residue definitions for the
> > various nonstandard components, and I can dock them (BDNA created
> > with nab). But I can't generate a topology file for the resulting
> > complex, seemingly because I have substantial atom overlap. Leap
> > complains of missing angle and dihedral terms, some of which don't
> > make sense....
> I don't think LEaP makes any use of geometry (or atom overlaps, etc.) in
> determining what angles and dihedral parameters it needs. So it should not be
> inhibited by the lack of a good starting model. You can use the "edit"
> command in LEaP to see visually what bonds are present, or the "desc" command
> to get a printed list. Maybe studying these will help you to figure out what
> is wrong with the residue definitions you have. If you can't figure it out,
> post a sample error message and the smallest construct that shows the problem.
> ...good luck...dac

Sure enough, I botched the definition of the topology in the prep
file for the modified G to which the propano group is bonded.
When I just let it be an ordinary internal G and did a LEaP
"remove" on the N2 hydrogen which is replaced in the adducted G,
LEaP was much happier. Now that I have topology and coordinate
files, I can proceed to remove the steric clashes.

Thanks everyone. Several good ideas were suggested, some in
private email. I don't believe these more sophisticated ideas
will be needed, however. Hopefully a simple sequence of
minimizations and MD runs will do the job.

Bud Dodson

M. L. Dodson                      
409-772-2178                                FAX: 409-747-8608
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Received on Fri Jul 02 2004 - 19:53:01 PDT
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