Sekar Ramachandran wrote:
HI,
I have run an Md simulation of the Wild-type and the
mutant forms of a protein. I would like to analyze the
simulations for any structural changes that might have
occured upon mutation. I have carried out the usual
rmsd and rmsf analysis and observe changes. I want to
know whether there is any to look at changes in side
chain interaction during the simulation.
Thanks a lot
Sincerely
there is g_saltbr and g_hbond
you may also try essential dynamics of the backbone of your protein
(g_covar)
Sekar Ramachandran
Research Associate
316 Baker Laboratories
DEpartment of Chemistry and Chemical Biology
Cornell University
Ithaca 14853
phone:607-254-6767
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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