[gmx-users] Residue-Residue interaction

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 28 08:53:00 CET 2006

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 
> 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.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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