# This scripts performs preparation and equilibiration of open-state PDZ3 domain for MD simulation

# Download PDB and prepare topology files

cd input
./makePDB01.sh
./makeTOP02.sh
./solvWAT03.sh
./addION04.sh

# Then the follwing directry are generated.
# PDB01/  TOP02/  WAT03/

ln -s WAT03/PDZ3_holo.top initial.gro
ln -s WAT03/PDZ3_holo.top topol.top

# Edit topol_restraint.top system.txt

cd ..

qsub 10steps_preparation.sh

# Then the follwing directories are generated.

step01_initial_minimization_of_mobile_molecules/  step03_initial_minimization_of_large_molecules/    step05_final_minimization_of_system/            step07_continued_relaxzation_of_large_molecules/  step09_unrestrained_relaxzation/
step02_initial_relaxzation_of_mobile_molecules/   step04_continued_minimization_of_large_molecules/  step06_initial_relaxzation_of_large_molecules/  step08_relaxzation_of_non-backbone_atoms/         step10_final_density_stabilization/

./density_stability.sh

# Then density.eps is generated.