[gmx-users] Position restrain of protein and membrane

[Justin A. Lemkul]

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/1050715198@Middle5/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null>
>  >>
>  >>
>  >>------------------------------------------------------------------------
>  >>
>  >>_______________________________________________
>  >>gmx-users mailing list    gmx-users at gromacs.org
>  >>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 gmx-users-request at gromacs.org.
>  >>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/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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

========================================