AMBER Archive (2003)

Subject: Re: how to restrain base pair

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 28 2003 - 14:14:49 CDT

On Mon, Apr 28, 2003, Shuang Ding wrote:

> When I am running MD simulation of 11mer DNA at constant pressure, the two
> strands become apart. So I want to use restraint on Watson-Crick base pairs.
> How to make restraint on base pair?

It should not be necessary to add such restraints for DNA simulations at
room temperature. If your strands are coming apart, there may be some
other problem with the simulation, which should be checked.

If you do need to add restraints, see section 5.9 (pp. 112-116) of the Users'
Manual.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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