From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
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 <dhacademic_at_gmail.com> 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 http://www.ks.uiuc.edu/~eschrein/ =============================================================================
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