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. > >-Justin > >> >> >> >>Ebay >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL >> PROTECTED]/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null> >> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list [email protected] >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the www interface >>or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >-- ======================================== > >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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