AMBER Archive (2007)

Subject: Re: AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9)

From: David A. Case (case_at_scripps.edu)
Date: Sun Feb 11 2007 - 00:57:27 CST

On Fri, Feb 09, 2007, Chengwen Chen wrote:

> I am modeling DNA duplexes in explicit model. Since one of the terminal
> bases flipped out after MD simulation, I try to use distance restraint on
> terminal WC of the duplex using weight of restraint at 1.0. But I am not
> sure about the way I make the input file, and the value of restraint
> weight. Is is large enough? I had tried 10.0, but the MD simulation quit
> with error. Can you give me some suggestions?

Note that the effective force constant is the product of rk2 (or rk3)
and the REST weight given in the weight change cards. Since you set
rk2=20, you already have a strong restraint even with a weight of 1.0;
giving a weight of 10, gives a net force constant of 200, roughly
equivalent to a covalent bond.

Since you just say the MD "quit with error", and gave no details, it's
not really possible to say very much that is helpful. Generally, with
restraints you have to look at the energies you get in each individual
situation to know if the force constants are appropriate are not.
Remember that these are "artificial", so there is no obvious right or
wrong answer about how strong they should be.

...dac

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