GROMACS-A Molecular Dynamic Approach

Once all this steps are done then start with the command section

COMMANDS :

1. command : grep -v HOH 1aki.pdb > 1AKI_clean.pdb

Files generated in folder : 1AKI_clean.pdb

2. command : gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
Over here a list of forcefield will appear. Type 15 as to select OPLS FORCE FIELD AND PRESS ENTER.
Files generated in folder : 1aki_processed.gro , posre.itp , topol.top

3. command : gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic
Files generated in folder : 1aki_newbox.gro

4.command : gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

Files generated in folder : 1aki_solv.gro , #topol.top.1#