AMBER Archive (2009)

Subject: Re: [AMBER] Creating conditions for biased MD

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 22 2009 - 13:01:39 CDT

The rectified helix has changed both baricenter and orientation. What
I was trying with Chimera was to superimpose it to the bent helix,
than remove the latter and get a pdb of the ensemble. Superimposition,
viewed as backbone, is not bad as far as the occupied "tube" is
concerned, giving me hope that leap could accept this ensemble. Then
some biased MD.

I have no experience with steered MD, can't imagine if, under the
described conditions, the rectified helix could serve as a template,
instead of a brutal replacing of helices.

francesco

On Wed, Apr 22, 2009 at 6:19 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
> I suspect the 'combine' command superimposes. In xleap a molecule
> can be selected by selecting one atom then using the option to select
> enclosing molecule. Then the molecules can be dragged apart and
> positioned. Some find this easier to do in other molecule editors.
>
> Bill
>
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