Re: [AMBER] Restrained MD

From: Carlos Simmerling <>
Date: Thu, 14 Jul 2011 17:22:21 -0400

 a few questions come to mind-

- how strong is the real-world binding of the peptide?
- are all of the heavy atoms well determined in your initial structure?
- are there any uncertainties about protonation states?
- is it possible that your equilibration protocol was not gentle enough?

with regard to your question, you can use restraints where the enzyme is in
the "fitmask" and the peptide is in the "rmsmask" and it will best-fit the
enzyme and keep the peptide in the same location relative to the enzyme as
it was at the start. check the manual for details.

On Thu, Jul 14, 2011 at 12:10 PM, Ozen, Aysegul

> 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
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Received on Thu Jul 14 2011 - 14:30:03 PDT
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