lec11

Merging the ligand file with protein:
-------------------------------------
1. After the application of force field, a .gro file is generated for the force field applied ligand. The 'editconf' module is used for this role:

			$ gmx editconf -f jz4_ini.pdb -o JZ4.gro

2. After this, the atomic coordinates of the ligand is manually added after the coordinates of the protein atoms.

													   .
				. . .		. . .		. . .		   .
			163ASN    OT1 2613   0.624  -0.616  -0.140 |-----> Coordinates of the protein atoms.		
			163ASN    OT2 2614   0.683  -0.703  -0.011_|
			1JZ4     C1    1   2.429  -2.412  -0.007 ]
								.					 .
								.					 .-------> Coordinates of the ligand atoms.
								.					 .
			1JZ4    H18   28   2.431  -2.365  -0.406_|
		   5.99500   5.19182   9.66100   0.00000   0.00000  -2.99750   0.00000   0.00000   0.00000	---> Box coordinates.

3. At the start of a .gro file, the number of atoms is specified. Since the ligand atoms are added, number of atoms must be modified accordingly. In the current
case, the ligand has 28 atoms, and the protein has 1614 atoms. So the combined number of atom is 1642, which is specifed accordingly.


			LYSOZYME
 No. of <--- 2642
 atom		    1MET      N    1   0.556  -1.596  -0.893
 modified	    1MET     H1    2   0.522  -1.511  -0.855
			    1MET     H2    3   0.520  -1.608  -0.986
								.
								.
								.

4. The then current topology file has to be modified as well. The ligand topology file which is jz4.itp in the current scope has to be added through include
directive. Its better to add the ligand position restrain file after the protein position restrain file as shown bellow:

				. . .	. . .	. . .
			; Include Position restraint file
			#ifdef POSRES
			#include "posre.itp"
			#endif

			; Include ligand topology
			#include "jz4.itp"
				. . .	. . .	. . .


5. Similarly the ligand parameter file - jzr.prm in this case, have to be added using the include directive. This should be added after the directive adding the
force field parameters:

				. . .	. . .	. . .
			; Include Position restraint file
			#ifdef POSRES
			#include "posre.itp"
			#endif

			; Include ligand topology
			#include "jz4.itp"
				. . .	. . .	. . .

6. A typical Gromacs topoly file ends with specifiying which molecules are present and how many. Since the combined file includes one additional JZ4 molecule,
this too has to be manually added:

		...		...		...
			[ molecules ]
			; Compound        #mols
			Protein_chain_A     1
			JZ4                 1

The stps after this is largely similar to that without ligand.