grep 'ATOM' 3ATL.pdb > protein.pdb
grep 'HETATM 1631 CA' 3ATL.pdb > ca‐ion.pdb
cat protein.pdb ca‐ion.pdb > protein2.pdb

pdb2gmx -ff amber99sb -f protein2.pdb -o trp.pdb -p trp.top -water tip3p -ignh

editconf -bt octahedron -f protein2.pdb -o trp‐b4solv.pdb -d 1.0

genbox -cp trp‐b4solv.pdb -cs spc216.gro -o trp-b4ion.pdb -p trp.top

grompp -f em.mdp -c trp-b4ion.pdb -p trp.top -o ion.tpr