[gmx-users] problem in insertion of protein into lipid bilayer in proper orientation

[Justin A. Lemkul]

chris.neale at utoronto.ca wrote:
> Use gromacs 3 for the editconf -princ step.
> 

Or, if using Gromacs 4, apply a 90-degree rotation, as I indicate in the tutorial.

-Justin

> -- original message --
> 
> Dear justin
> 
>                     Thanks for tutorial on membrane protein simulation  . I
> am following your tutorial, everything is fine but problem came in
> concatanation .  After orrienting the protein by using editconf
> I did the concatanation process everything is fine but the file which I got
> after concatanation i.e system.gro  when I viewed this file in pymol the
> insertion is totally wrong the protein inserted parallel to bilayer
> hydrophobic core it is totally wrong I need protein should inserted
> perpendicular to lipid bilayer i.e from one side polar head of lipid to
> another side by crossing hydrophobic core of lipid .
> 
> can u suggest me right method to insert my protein into lipidbilayer in
> proper orientation before using  inflategro methedology.
> I am just stuck on that point .
> 
> I am eagerly waiting  for your  reply.
> 
> Thanks a lot in advance.
> 
> _______________________________________________
> 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 thewww 
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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