MD_prep

NTOMP=$1


#using AMBER99SB-tip3 according to https://onlinelibrary.wiley.com/doi/full/10.1002/jccs.201900148
echo 5 | gmx pdb2gmx -ignh -f COMPLEX.pdb -o COMPLEX_processed.gro -water tip3

gmx editconf -f COMPLEX_processed.gro -o COMPLEX_newbox.gro -c -d 1.0 -bt cubic #create box

gmx solvate -cp COMPLEX_newbox.gro -cs spc216.gro -o COMPLEX_solv.gro -p topol.top #add water

gmx grompp -f ions.mdp -c COMPLEX_solv.gro -p topol.top -o ions.tpr -maxwarn 2 #create atomic desc file

echo 13 | gmx -quiet -backup genion -s ions.tpr -o COMPLEX_solv_ions.gro -p topol.top -pname NA -nname CL -neutral

gmx grompp -f minim.mdp -c COMPLEX_solv_ions.gro -p topol.top -o em.tpr    #create em.tpr

gmx mdrun -ntmpi 1 -ntomp $NTOMP -pin on -v -deffnm em  #run energy minimization

gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr          #create nvt.tpr