VMD-L Mailing List

From: Lady L. Gutierrez (ladyg30_at_eden.rutgers.edu)
Date: Wed Feb 23 2005 - 18:54:11 CST

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.