AMBER Archive (2004)

Subject: AMBER: peptide-DNA crosslink modeling

From: M. L. Dodson (
Date: Thu Jul 01 2004 - 16:51:24 CDT

Hello ambers,

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 (there are no such combinations in the pdb files).
That's why I think it must be because of the atom clashes. The
prep files for the nonstandard residue definitions pass parmchk.

The peptide does not "fit" in the minor groove of canonical BDNA,
so I don't see an obvious way to create a starting structure that
is free of steric overlap.

Does anyone have a good idea of a (topology file-independent) way
to create a starting structure? If I were clever enough, I might
be able to come up with some appropriate atom expressions to
create an bounds matrix to do some distance geometry runs in nab,
but what those expressions might be is not at all obvious. That's
the only thing I've been able to come up with so far.

Any ideas would be appreciated.

Bud Dodson

M. L. Dodson                      
409-772-2178                                FAX: 409-747-8608

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