Call minimise on the wildtype as well as SCWRL and FOLDX mutant structures. Also iterate another five rounds for each structure

callMinimise.sh

#!/bin/bash
function iterate()
{
        BASEI=$1
        /opt/SS12-Practical/minimise/minimise $BASEI.pdb ${BASEI}_it1.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it1.pdb ${BASEI}_it2.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it2.pdb ${BASEI}_it3.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it3.pdb ${BASEI}_it4.pdb &>> ${BASEI}_it.log
        /opt/SS12-Practical/minimise/minimise ${BASEI}_it4.pdb ${BASEI}_it5.pdb &>> ${BASEI}_it.log
}

#FOLDX files
BASE="2gjxA_secondD_repaired_"

rm -rf ./foldx/
mkdir foldx
cd foldx

for i in {1..10}; do
        /opt/SS12-Practical/scripts/repairPDB ../../FOLDX/$BASE$i.pdb -noh -nohoh > $BASE${i}_nohnohoh.pdb
        /opt/SS12-Practical/minimise/minimise $BASE${i}_nohnohoh.pdb $BASE${i}_nohnohoh_min.pdb &>> min_log
        iterate $BASE${i}_nohnohoh_min

        /opt/SS12-Practical/scripts/repairPDB ../../FOLDX/WT_$BASE$i.pdb -noh -nohoh > WT_$BASE${i}_nohnohoh.pdb
        /opt/SS12-Practical/minimise/minimise WT_$BASE${i}_nohnohoh.pdb WT_$BASE${i}_nohnohoh_min.pdb &>> wt_min_log
        iterate WT_$BASE${i}_nohnohoh_min
done

#SCWRL
cd ../
rm -rf ./scwrl/
mkdir scwrl
cd scwrl

for i in R178H R178C P183L D207E S293I F434L L451V E482K L484Q E506D; do
        /opt/SS12-Practical/scripts/repairPDB ../../SCWRL/SCWRL_$i.pdb -noh -nohoh > SCWRL_${i}_nohnohoh.pdb
        /opt/SS12-Practical/minimise/minimise SCWRL_${i}_nohnohoh.pdb SCWRL_${i}_nohnohoh_min.pdb &>> min_log
        iterate SCWRL_${i}_nohnohoh_min
done