[gmx-users] Regarding .itp file to the system

[Alex Mathew]

Dear Justin,
Thanks for  your previous answer i quoted below

"1. Process the protein with pdb2gmx and obtain a .top and coordinate file in
whatever format you like.
2. Generate a ligand topology, #include its .itp file in the .top
3. Append the ligand coordinates to those of the protein from step (1); again
format is irrelevant"

i have done first two steps ,i done with pdb2gmx for the protein

added .itp file to topol.top as

*; Include ligand topology
#include "molecule.itp"*

i don't understand the third step ,could you please elaborate little
more,sorry i couldn't understand it.


Thanks