AMBER Archive (2004)

Subject: Re: AMBER: peptide-DNA crosslink modeling

From: David A. Case (case_at_scripps.edu)
Date: Fri Jul 02 2004 - 00:01:40 CDT

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

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