lec12

After the combined .gro file and corresponding topololgy file for the protein-ligand complex has beed achieved, the regular preparation steps follow:

Defining the box
----------------
Command:
		$ gmx editconf -f cmpl_3htbJZ4.gro -o box.gro -bt cubic -d 1.0

Here,
	'-f' option specified the input file name: cmpl_3htbJZ4.gro
	'-o' option specified the output file name: box.gro
	'-bt' specifies box type. Here 'cubic' box type is chosen.
	'-d' specifies 1.0nm of periodic boundary.

Note that, this time the '-c' option, that specifies the central position for the protin is not specified, since both protien and ligand are being studied.


Solvation
---------
Command:
		$ gmx solvate -cp box.gro -cs spc216.gro -p topol.top -o sol.gro

This step is indentical with the step without the ligand, as reflected to the command.


Neutralization
--------------
Command:
		$ gmx grompp -f ions.mdp -c sol.gro -p topol.top -o ions.tpr
		$ $ gmx genion -s ions.tpr -o ions.gro -p topol.top -pname NA -nname CL -neutral

Both steps of the neutralization are completely identical to these step without ligand. So, the detail fo these steps are not discussed further.


Energy minimization and analysis
--------------------------------
$ gmx grompp -f em.mdp -c ions.gro -p topol.top -o em.tpr
$ gmx mdrun -deffnm em -v
$ gmx energy -f em_3htb.edr -o em_3htb.xvg		# Analysis.

Like previous two steps, energy minimization too, is identical with non ligand simulation.