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

[chris.neale at utoronto.ca]

Use gromacs 3 for the editconf -princ step.

-- 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.