grep 'ATOM' 4BX5.pdb > protein.pdb

pdb2gmx -ff amber99sb -f protein.pdb -o avidin.pdb -p system.top -water tip3p -ignh

acpype -i biotin.pdb
//copied "biotin_GMX.gro" and "biotin_GMX.itp" to home directory

//edited system.top to #include "biotin_GMX.itp"

editconf -bt octahedron -f avidin.pdb -o avidin-b4solv.pdb -d 1.0

genbox -cp avidin-b4solv.pdb -ci biotin_GMX.gro -nmol 10 -cs spc216.gro -p system.top -o system.gro

//added "biotin             10" to system.top

grompp -f em.mdp -c system.gro -p system.top -o em.tpr -maxwarn 2
mdrun -v -deffnm em
//Error: A charge group moved too far between two domain decomposition steps

trjconv -s em.tpr -f em.trr -o em.xtc -pbc nojump
vmd system.gro em.xtc
//visualization shows that all atoms (water and biotin) are making unusual bond angles and lengths.