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
--
========================================
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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