[gmx-users] how to simulate the transformation of loop

[Justin Lemkul]

On 4/16/13 9:15 PM, aixintiankong wrote:
> Dear,
>         In my system ,the loop is  part of the active pocket  of the protein. when the ligand is absent, the loop is disordered and if the ligand is present , the loop can transform into helix. i don't know how to the simulate the state of the shape of the loop at the different the situation. During the simulation, should i set  the specific parameters in the mdp , such as temperature or the others
>        please give me some advice .thank you !
>

Presumably, if the segment is a loop and you add the ligand, you will observe a 
conversion to helix, and vice versa.  There are no magic keywords or settings to 
make this happen; it is a spontaneous behavior that should be observable during 
the simulation.  Note that structural conversions like this are heavily 
dependent upon the force field.  Make a wise choice.

-Justin

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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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