Journal structure based mutation analysis (PKU)

runAllMinimiser.sh

Usage: runAllMinimiser.sh <filestem>
where filestem is the name of the pdb-file you want to start your minimization on, without the .pdb-ending. The rest of the script is done automaticly. <source lang="bash">

1. !/bin/sh
2. only for use in the biolab

if [ -f /opt/SS12-Practical/minimise/minimise ]; then

echo minimise has/home/hpc/pr58ni/di34faw been located
echo starting for ${1}.pdb
i=0
while [ $i != 5 ]; do
 echo iteration $i
 if [ $i -eq 0 ]; then
  echo "calling: /opt/SS12-Practical/minimise/minimise ${1}.pdb ${1}_min1.pdb > minimise${1}_1.log 2> /dev/null"
  /opt/SS12-Practical/minimise/minimise ${1}.pdb ${1}_min1.pdb > minimise${1}_1.log 2> /dev/null
 else
  next=$((i+1))
  echo "calling: /opt/SS12-Practical/minimise/minimise ${1}_min${i}.pdb ${1}_min${next}.pdb > minimise${1}_${next}.log 2> /dev/null"
  /opt/SS12-Practical/minimise/minimise ${1}_min${i}.pdb ${1}_min${next}.pdb > minimise${1}_${next}.log 2> /dev/null
 fi
 i=$((i+1)) 
done
fi
echo end

</source>

prepare for Gromacs

<source lang="bash">

#done on the lrz...
#!/bin/bash
scriptdir=$HOME/AGroS
dir=$HOME/minimizeGromacs

for struct in `ls $dir/Models/*.pdb` ; do
       tmp=$(basename $struct)
        basestruc=${tmp%\.*}
       $scriptdir/repairPDB $struct -jprot > $dir/Models/$basestruc\_jprot.pdb
       $scriptdir/repairPDB $struct -seq |tr 'A-Z' 'a-z' > $dir/Models/$basestruc.seq
       $scriptdir/scwrl -s  $dir/Models/$basestruc.seq -i $dir/Models/$basestruc\_jprot.pdb -o $dir/Models/$basestruc\_scwrl.pdb
       $scriptdir/repairPDB $dir/Models/$basestruc\_scwrl.pdb -jprot > $dir/Models/$basestruc\_nh.pdb
       rm $dir/Models/$basestruc\_jprot.pdb $dir/Models/$basestruc\_scwrl.pdb $dir/Models/$basestruc.seq
done


for forcefield in amber03 ; do #amber03 charmm27 oplsaa ; do
        mkdir -p $dir/Models/$forcefield/tpr/
        for struct in `ls $dir/Models/1*_nh.pdb` ; do
                strucname=${struct%\.*}
                tmp=$(basename $struct)
                basestruc=${tmp%\.*} 

                cd $dir/Models/$forcefield
                echo "call pdb2gmx"
                pdb2gmx -f $strucname -o $dir/Models/$forcefield/$basestruc.gro -p $dir/Models/$forcefield/$basestruc.top -water tip3p -ff $forcefield > $dir/logs/pdb2gmx\_$basestruc\_$forcefield.log
                grompp -v -f $dir/gromacs$i.mdp -c $dir/Models/$forcefield/$basestruc.gro -p $dir/Models/$forcefield/$basestruc.top -o $dir/Models/$forcefield/tpr/time/$basestruc$i.tpr > $dir/logs/grompp\_$basestruc\_$forcefield\_time$i.log
        done
done

</source>