[gmx-users] Editing of the existing system

[James Starlight]

Justin,

31 марта 2012 г. 18:18 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

>
> Start by inspecting the initial configuration in the vicinity of these
> atoms. Something is likely clashing here.


Yes, I've checked both of the proteins and found that the problem atoms
were situated exactly in the docked region of the both proteins. So It
seems that there are some clashes between atoms in the docked site. By the
way this site of the first protein ( Receptor) consist of 2 flexible loops
and the rigid helix from the second protein. ( fragment of G-protein) Might
the energy minimisation solve this problem generally ? ( e.g by means of CG
minimisation to very low forces aplied on atoms). Is there any possible
ways to change conformation of the flexible loops during minimisation\
equilibration phases without aplication of any external forces?

James
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