[gmx-users] Insertion of protein in lipid bilayer

[John Simms]

Hi nagaraju,
What you need to do is to change the DPPC to DPP in the command line,
perl make_hole.pl -f dppc.pdb -o outbilayer.pdb -r 1.4 -lipat P8 -lipid DPPC -cx 3.2 -cy 3.2 
as this is what is defined in the PDB file. After you have done this you will need to change the number of DPP molecules in the .top file. Also make such that you renumber the last water atoms to be consistent with the input file AFTER the initial hole has been made.
Cheers
John