I think your question is too general. So: what do you want to do and how? Do you need software for simulation or analysis of experimental results? What do you mean by "seperation of DNA helix"?
If you supply more information, you will get help more easily.
Dear Ernst,
I want to know about the software for simulation. Actually I want to find out the active sites in DNA , and I should separate them from helix. after that I should dock with a drug. For all these things i need free software.
I presume you want to know the free energy for the process of denaturation. Am I right?
Well, that only means (Delta G calculation) you are going to run a Molecular Dynamics simulation. There are several FREE packages for doing that, one of them is CPMD (very exhaustive software, computing demanding though). Take a look at Biophysics Urbana http://www.ks.uiuc.edu/Training/Tutorials/. Lots of drawings and animations. Don't know how useful it may be. The MD calculations need some computer time, be prepared.
Dear Victor,
Thank you so much. The above link is very useful. I have a doubt. I took a NMR structure from pdb. I have to solvate it with 400 water molecules. Is there any free solvation software for this..
There are a number of these, some won't work as you want. Here is a good one, but you will have to export and edit coordinates;
http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
You can download VMP for free.
400 H2O is a demanding task :-)
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