[gmx-users] Editing of the existing system

James Starlight jmsstarlight at gmail.com
Sat Mar 31 20:05:24 CEST 2012


Sorry that I can't provide you with such information now because that data
have been left in my lab workstation. Tomorrow I'll find all this logs and
attach it to this topic. Also I've run more properly CG minimisation (
EMtool=0.01) in double precission mode. I'll check this results too and
attach all logs here.

Many thanks again for help


31 марта 2012 г. 21:57 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

> 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
> --
> ==============================**==========
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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