[gmx-users] best way to create a pdb file.

[Senthil Kandasamy]

What is the easiest way to accomplish the following?

I have a pdb file of a lipid bilayer. I need to insert a protein bundle 
into this bilayer. I have the pdb coordinates of the protein bundle 
also. Now, I edit the lipid pdb file to create a hole (that would 
approximately fit my bundle) at the center. Both the bundle and the 
lipids are centered using editconf. Upto this point, I have two pdb 
files. Now, what is the easiest way to create a single pdb file of this 
structure (That would essentially have the bundle inserted into the 
lipid layer)

I have to go through a lot of manual manipulations to be able to do that 
at this point. IS there an easier way to accomplish this?

Thanks.

Senthil