VMD-L Mailing List

From: geetha9999_at_aol.com
Date: Thu Feb 11 2010 - 13:37:08 CST

Hi All:

My protein of interest has been crystalized and available in pdb database. I want to mutate only one amino acid and simulate the crystal structure with NAMD???? Is this feasible.

Similar work was done using InsightII/homology module but it is expensive. I need your advise. Is any plugin available? Have anybody done it? This will be very helpful.

Then I want to calculate the distance between two amino acids located at the active site for both wild and mutant type proteins in the simulated MD.

Is there a substitute for InsightII/affinity module, InsightII/biopolymer module or InsightII/binding site module available free?

I appreicate your help.

Thanks
Geetha