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

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 11 13:47:03 CEST 2009

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.


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


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