[gmx-users] help regarding simulation

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 4 16:19:53 CET 2011

onetwo wrote:
> Hello All,
> I want to know one thing that if MD could be used in my case, i have a 
> protein for which crystal structure is known with a conenzyme bound to 
> it. It is given in literature that related proteins of this family shows 
> large conformational change near the substrate binding region when the 
> substrate binds to the protein.
> In absence of the crystal structure, if doing simulation with the 
> protein complexed with the coenzyme and the docked substrate will be 
> useful? , i.e, if this complex with the help of the simulation could be 
> capable of displaying such conformational change ? or what could be the 
> probable limitaions ?

Possibly.  The limitation is time.  Conformational changes are generally slow, 
so your simulations would likely have to be fairly long.


> Regards and thanks for your time.
> <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle?>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list