[gmx-users] Editing of the existing system

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 31 19:57:00 CEST 2012

James Starlight wrote:
> Justin,
> 31 марта 2012 г. 18:18 пользователь Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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?

Proper EM should resolve such clashes, but under normal circumstances that 
should have happened already.  You may have to do EM in vacuo before adding any 
solvent to allow for proper resolution of clashes.  I'm only guessing at this 
point.  I have asked twice for the output of your previous EM attempts, which 
would give me a much better idea of where things stand.  Since you haven't 
answered those questions, I'll leave it up to you to try to resolve.  Good luck.



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


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