From: Jérôme Hénin (
Date: Thu Feb 24 2005 - 02:04:50 CST


I too have a question for you: what is the activation mechanism of the
receptor I am studying?

Okay, what I really mean is:
1) Your questions are not connected to VMD
2) People on the list may answer some of the first ones by giving you clues
about methods you should use, but they are not likely to perform your
research for you, which is what you seem to be asking from them.

What about a post to NAMD-list asking, "Can I simulate the anchoring of RNA
polymerase to DNA using NAMD, and what kind of protocol should I use?". I am
not sure you will get many useful answers, because the question is far from
easy, but at least you will be asking in the right place.


Le jeudi 24 Février 2005 01:54, Lady L. Gutierrez a écrit :
> Hello All,
> I am attempting to simulate the mechanism that reveals RNA polymerase
> docking to DNA. How would I go about in finding the correct way that the
> ratcheting mechanism occurs? I have already downloaded RNA polymerase and
> DNA pdb files and have created the psf files using NAMD.. What is the next
> step or where can I find more information regarding this matter? Also, a
> couple other questions:
> Is there a center of rotation for this ratcheting mechanism?
> Does it torque?
> Is the RNA ratcheting uniform?
> Thanks in advance.

Jérôme Hénin
Equipe de Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS
Tel : (33) 3 83 68 43 95        Fax : (33) 3 83 68 43 71