#!/bin/bash
#
# Code by  venkentom@gmail.com
#
# Licenced by the GPL General Public License
# Have a look at:
# http://www.gnu.org/copyleft/gpl.html
# For more information about the GPL License
#
# I am not responsible for what this code does to your hw/sw/mind
# Use at your own risk
# 

#Put gromacs commands after this line

DIR=`pwd`

#Config
NPROCS=2

# !! *** same procedure as in TM19_sol, now with polarized ff *** !!

# used TM19 created in moe, then sed chain name in pymol using 
#		alter (all),chain='A'
#		sort 
# then make martini topology: 
# ./martinize.py -f TM19_sed.pdb -o system_vaccum.top -x TM19_pol_CG.pdb -dssp /Applications/DSSP_MAC.EXE -p backbone -ff martini22p

# editconf -f TM19_pol_CG.pdb -o editconf.pdb -bt cubic -d 1 -c

#change martini.itp to #include "martini_v2.2.itp" in system_vaccum.top
# grompp -f minimization_vaccum.mdp -p system_vaccum.top -c editconf.pdb -o minimization_vaccum.tpr -maxwarn 1
# mdrun -deffnm minimization_vaccum -v

source /Home/ii/venken/.bashrc

for i in {11..20}
do

mkdir $i
cp ../system.top $i
cp ../system_noW.top $i
cp ../*.itp $i
cp ../popc_single.gro $i
cp ../polarize-water.gro $i
cp ../minimization.mdp $i
cp ../assemble.mdp $i
cp ../genion.mdp $i

genconf -f ../TM19_D0.pdb -rot -o $i/genconf_${i}.gro

j=$[ RANDOM % 9 ]
k=$[ RANDOM % 9 ]
l=$[ RANDOM % 9 ]

cd $i
editconf -f genconf_${i}.gro -o editconf_${i}.gro -box 9 9 9 -translate $j $k $l -noc
genbox -cp editconf_${i}.gro -ci popc_single.gro -nmol 128 -try 500 -o genbox_${i}.gro

grompp -f minimization.mdp -c genbox_${i}.gro -p system_noW.top -maxwarn 10 -o min-init_${i}.tpr
mdrun -deffnm min-init_${i} -v 

genbox -cp min-init_${i}.gro -cs polarize-water.gro -o waterbox_${i}.gro -maxsol 1500 -vdwd 0.21

grompp -f genion.mdp -c waterbox_${i}.gro -p system.top -o system_neutral_${i}.tpr
genion -s system_neutral_${i}.tpr -o system_neutral_${i}.gro -p system.top -pname NA- -nname CL- -neutral -conc 0.000001 << EOL
PW
EOL

make_ndx -f system_neutral_${i}.gro -o index.ndx <<EOL
1 | 18
name 22 Protein
del 1
19 | 20
q
EOL

grompp -f minimization.mdp -c system_neutral_${i}.gro -p system.top -maxwarn 10 -o min-solvent_${i}.tpr 
mdrun -deffnm min-solvent_${i} -v 

grompp -f assemble.mdp -c min-solvent_${i}.gro -p system.top -maxwarn 10 -o assemble_${i}.tpr -n index.ndx
mdrun -deffnm assemble_${i} -v

rm \#*

cd ..

done