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.
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