AMBER Archive (2003)

Subject: Re: AMBER: restrain

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 07 2003 - 10:34:21 CST

On Fri, Nov 07, 2003, Vlad Cojocaru wrote:

> I am simulating a nucleic acid with 2 helical arms. I would like to
> introduce restraints for the angle between the 2 helical axis. Could
> somebody suggest a way how to do that?

You could use an angle restaint in sander. Choose two atoms near the ends
of the arms, and the central atom near the hinge point. Then the angle
restraints would help keep that angle fixed.

If there is no single hinge point between the two arms, then things are
more complicated, and you might need to code up your own restraints.

..good luck..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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