Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Tue Mar 07 2006 - 21:12:42 CST

Hi Vijay,
NAMD certainly can handle a simulation with DNA and protein. The
NAMD tutorial does not have any specific information on protein-DNA
interactions but it will certainly help you to get started on running
NAMD simulations. You can find it here:

http://www.ks.uiuc.edu/Training/Tutorials/

To run your simulations, you will need topology and parameters for
DNA, which can be found at Alex MacKerell's website:

http://www.pharmacy.umaryland.edu/faculty/amackere/force_fields.htm

Also, the NAMD mailing list might be a good place to search or
address questions to should you run into problems with your simulations:

http://www.ks.uiuc.edu/Research/namd/mailing_list/

I hope this helps start you off,
Tim

------------------------------------
hello..
i am new to namd. i have taken up molecular dynamics and simualtion
as my
final year project. I want to know the complexity that NAMD can handle.
i want to simmulate a dna- protein interaction with water as
enviornment. My
computaional facilities are a 8-node Beuwolf cluster.

is this feasible using NAMD?

i have tried a molecular dynamic simmualtion before but it was using
GROMACS.
can you please suggest me the requirements and sources i can refer
for this
project.

Thanking you
Vijay Santhosh Kumar
IV year Btech Bioinformatics
VIT , vellore.
**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**