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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.<BR>
Can you give me suggestion <BR>
Thanks in advance. <BR>
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>minnale wrote:<BR>
>> Hi all,<BR>
>>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.<BR>
>>Thank you.<BR>
><BR>
>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.<BR>
><BR>
>-Justin<BR>
><BR>
>><BR>
>><BR>
>><BR>
>>Ebay <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null><BR>
>><BR>
>><BR>
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>><BR>
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>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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