AMBER Archive (2006)

Subject: Re: AMBER: Restraints of the strand-endings?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Nov 14 2006 - 16:19:06 CST

> I did a MD with weak restraints on a DNA/coval=
> entyl bound drug complex and as soon as I switch to an MD with a MD with c=
> onstant pressure without SHAKE, the endings of the double strand become un=
> stable.

If you are using TIP water, SHAKE on H is required.

Bill

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