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 - 09:30:03 PDT
