AMBER Archive (2005)

Subject: RE: AMBER: Problems Binding Protein to DNA

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Wed Mar 09 2005 - 05:16:44 CST

>Dear AMBER users,
>
>I'm an undergraduate student new to AMBER working with the allenlab
>(www.theallenlab.com). I've been having problems running a MD
>simulation of protein bound to DNA. Is there anyone out there that
>will lend some insight into this problem? Thanks much for your help!
>

Could you be more elaborate on your problem. When working with DNA, in any
case, you have to be very careful with few things:

(1) Counterions, and while you minimize the system, taking restraints
gradually due to highly charged nature of the system

(2) You might almost want to work with Boxes and PBCs, because you might
want to see a more realistic behavior of any water molecules involved in
Protein-DNA interactions, which are very crucial in these systems

There are may good, authoritative reviews and articles on this subject >>

a) Norberg J, Nilsson L
Molecular dynamics applied to nucleic acids
ACCOUNTS OF CHEMICAL RESEARCH 35 (6): 465-472 JUN 2002

b) Norberg J, Nilsson L
Advances in biomolecular simulations: methodology and recent applications
QUARTERLY REVIEWS OF BIOPHYSICS 36 (3): 257-306 AUG 2003

c) Nilsson, L. (1998) Protein Nucleic Acid Interactions. In "Encyclopedia of
Computational Chemistry" (Eds. P. von Ragué Schleyer, N.L. Allinger, T.
Clark, J. Gasteiger, P.A. Kollman, H. F. Schaefer III) , Vol. 3, 2220-2229,
John Wiley & Sons

Hope this helps,
Cheers
Vineet

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