[gmx-users] Position restrain of protein and membrane

[Justin A. Lemkul]

minnale wrote:
>  
> Thanks for reply Justin, can I do this way first I will keep PR on popc 
> later protein, I dont want keep PR on water.Can I do like this?

You could, but I don't see the point.  In equilibrating membrane protein 
systems, it is very important to optimize the lipid positions around the protein 
at the outset of the simulation (i.e., packing).  So allowing the protein to 
move unrestrained while restraining the lipids makes no sense (and you will 
probably generate some artificial interactions).  You will want to apply PR to 
the protein, allowing the lipids to pack around it, then remove the PR from the 
protein and proceed with data collection.

-Justin

> Thanks in advance.
> 
> On Tue, 16 Sep 2008 Justin A.Lemkul wrote :
>  >
>  >
>  >minnale wrote:
>  >>Thanks Justin for your kind reply, you misunderstood my query,now I 
> am asking you clearly that, while doing membrane protein equilibration 
> steps on which system( either protein or membrane or both) I have keep 
> to position restrain? is there any conventional way to keep restrain? or 
> it can change according to ourselves. I hope you understood my problem.
>  >>Can you give me suggestion
>  >
>  >You can restrain whatever you like; typically just the protein is 
> restrained. Check the literature for common protocols.
>  >
>  >-Justin
>  >
>  >>Thanks in advance.
>  >>
>  >>
>  >>
>  >>
>  >>  >minnale wrote:
>  >>  >>  Hi all,
>  >>  >>I embedded protein into popc bilayer by using genbox command, in 
> equilibration I want keep restrain only on protein but not on popc? can 
> I do like this or is there any manditory steps to run membrane protein 
> equibration, if it is there, Can you tell me please.
>  >>  >>Thank you.
>  >>  >
>  >>  >Use "define = -DPOSRES" which is specified in the .top from 
> parameterizing the protein under pdb2gmx.  There's nothing special 
> (necessarily) for doing a membrane protein system, since all the 
> topology information for the protein generally comes before the 
> lipid/solvent stuff, anyway.
>  >>  >
>  >>  >-Justin
>  >>  >
>  >>  >>
>  >>  >>
>  >>  >>
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>  >>  >-- ========================================
>  >>  >
>  >>  >Justin A. Lemkul
>  >>  >Graduate Research Assistant
>  >>  >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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>  >-- ========================================
>  >
>  >Justin A. Lemkul
>  >Graduate Research Assistant
>  >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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================