[gmx-users] Position restrain of protein and membrane

[minnale]

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?
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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