Re: [AMBER] Restrained MD

From: Dmitry Nilov <>
Date: Fri, 15 Jul 2011 12:45:46 +0400

Hello, also you could try to apply harmonic restraint on the distance
between substrate and binding site residue (or residues). To do that
you can use steered molecular dynamics capability in Amber (see Manual
or Just set the
initial and final reference distance to be equal.

On Thu, Jul 14, 2011 at 8:10 PM, Ozen, Aysegul
<> wrote:
> Hello,
> I'm trying to set up an MD simulation using Amber 10 for a protein-substrate complex starting from an x-ray structure. The problem is that the protein has a very shallow binding site and the substrate is a 6-amino acid peptide and in about 20 ns, the peptide starts diffusing away from the binding site. The goal of this simulation is to get information about the local conformational space spanned by the substrate when it's bound to the enzyme. I would like to impose a reasonable/minimal restraint on the peptide just enough to prevent it from drifting away from the active site.
> I typically use restrained minimizations where the coordinates are harmonically restrained with respect to a reference set of coordinates. However, in this case, the reference is the enzyme and its coordinates are, of course, changing throughout the production phase. Could you have any suggestions on how to define this restraint on the substrate wrt the protein binding site region? Or any smarter way to set up this simulation?
> Thanks much!
> Aysegul Ozen
> PhD Student
> Biochemistry and Molecular Pharmacology
> University of Massachusetts Medical School
> 364 Plantation Street, LRB 827
> Worcester, MA  01605
> ph: (508) 856-2636
> _______________________________________________
> AMBER mailing list

Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
AMBER mailing list
Received on Fri Jul 15 2011 - 02:00:02 PDT
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