Re: impose restraint on the internal coordinate of protein

From: Eduard Schreiner (
Date: Mon Jun 21 2010 - 14:41:53 CDT

I think, this is not possible in NAMD (yet).
The closest to what you want to have is the extrabonds feature.
( you can see how it is used in the MDFF tutorial
You could use that to restrain all the backbone dihedrals. However, your
monomers will still not be real rigid bodies.


On Mon, Jun 21, 2010 at 1:43 PM, dhacademic <> wrote:
> Hi, I have a question about imposing restraint on protein.
> In my system, a dimer-of-dimer structure (protein) is merged in a water box,
> say dimer A (with monomer a and b) and dimer A' (with monomer a' and b'). I
> want to keep the structures as well as the relative orientation within the
> dimer, but to search the optimal orientation between the two dimers by MD
> simulations. How can I impose this kind of restraint in NAMD?
> Thanks in advance.
> Hao Dong

Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078

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