On 3/4/13 10:37 AM, Ewaru wrote:
Hi Justin,
Thank you for your prompt reply! As this is my first approach to molecular
dynamics, I still have lots of to understand but I'm constantly reading and
trying to work things out. I predicted 2 structures, one using Modeller, and
another one with I-Tasser. I followed your very informative tutorial for the
approach of energy minimization and equilibration using Gromacs. My mistake
for assuming that RMSD should fall within 0.1nm. I'm supposed to choose the
best model to proceed with docking. Is it okay if I run just a 10ns
simulation for both the predicted structure and then decide the best one by
comparing the stability of the protein, from the output of the RMSD and
radius of gyration?
Radius of gyration is probably not the best criterion here; I just demonstrated
it in the tutorial because it is a rather fool-proof program. RMSD is a decent
indicator of structural changes, but by itself doesn't necessarily indicate
convergence or tell you anything useful about the structure. You need to apply
some real biological knowledge before concluding which model is "best." Since
successful docking requires an accurate representation of the binding site, you
need to probably examine the stability of critical residues, interactions among
them, etc. There are far more metrics that can be assessed than just trivial
things like RMSD and Rg. The tutorial is by no means comprehensive (nor does it
claim to be), so spending some time in the literature and reading textbooks
about these techniques should be prerequisite.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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