[gmx-users] Position restrain of protein and membrane

minnale minnale_gnos at rediffmail.com
Tue Sep 16 06:23:22 CEST 2008

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 
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.
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>-- ========================================
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
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