From: Luis Rosales (
Date: Wed Feb 23 2005 - 22:55:20 CST


>From what you said on your mail, I would think that maybe normal mode analysis
would be more suited for your needs than a long molecular dynamics simulation.

>From the paper of Shure et al.:

"One major application of normal modes is the identification of potential
conformational changes. The method has also been used recently in the study of
membrane channel opening, the analysis of structural movements of the
ribosome, viral capsid maturation, transconformations of the SERCA1 Ca-ATPase,
tertiary and quaternary conformational changes in aspartate transcarbamylase
and the analysis of domain motions in large proteins in general."

There are several tools for NMA, including the Elnemo server
[], GROMACS, and (I think,) CHARMM.

Independently of the tool (NMA, molecular dynamics) that you choose for your
analysis, I think that an important step would be to compare several
structures of RNApol (unliganded, with nucleic acids, with
amanitin/inhibitors, etc).

If you happen to have a couple of structures of your particular molecule, you
could use DynDom to determine what segments are moving, what residues act as
hinges, etc... (By the way, dyndom has a domain motion database, maybe you
could find something interesting there...)

Also, have you looked the "molecule of the month" at the PDB site? (2003) even
if the information is too basic, at the end of the article there is a list of
PDB structures of RNApols updated until 2003.

Anyway, I hope that something of this could be helpful to you.

Kind regards,


---------- Original Message -----------
From: "Lady L. Gutierrez" <>
Sent: Wed, 23 Feb 2005 19:54:11 -0500 (EST)
Subject: vmd-l: RNA polymerase docking on DNA

> 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.
------- End of Original Message -------