Re: AMBER: peptide-DNA crosslink modeling

From: Carlos Simmerling <>
Date: Thu, 1 Jul 2004 21:42:48 -0400

what about using a zero (or nearly 0) force constant for
the linker bond, making the peptide initially outside the groove and
then adding in a flatwell harmonic distance restraint
corresponding to the bond. then you could reduce the position
of the upper limit to the harmonic slowly during an MD
run (easy with nmropt-1), pulling in the peptide into the groove.
after it was equilibrated you could go back to a normal bond treatment.

not sure if it would work, but you asked for ideas!
----- Original Message -----
From: "M. L. Dodson" <>
To: <>
Sent: Thursday, July 01, 2004 5:51 PM
Subject: AMBER: peptide-DNA crosslink modeling

> 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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Received on Fri Jul 02 2004 - 02:53:00 PDT
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