[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh at mech.sharif.ir]

Dear All
During researching Internet, I found justin and Anirban's tutorial
about embedding protein
in lipid membrane. It was useful and I appreciate them but I had one
question. as I understood, I should make some changes to protein pdb file
( 1r2h for Ex)
 before using it in  pdb2gmx command or the GROMACS can't
keep on and will be died with a fatal error ( something like adding cope
to the ends of the protein ). could
somebody please tell me what should I do ? by the way I found out that
Justin's
tutorial do something with xleap amber on the pdb file.
Please tell me how specifically I should revise my protein pdb file.

best regards
Ali khourshaei shargh (khourshaeishargh at mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran