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 >> > >> >> >> >> >> >> >> >>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 >> > >> >======================================== >> >> >> >>Rediff Shopping >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL >> PROTECTED]/2206641_2199021/2201651/1?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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