run_muts.sh

#!/bin/bash

for file in ../SCWRL/SCWRL*.pdb 2gjxA_secondD.pdb; do
        tmp=$(basename $file)
        basestruc=${tmp%\.*}
        perl ../repairPDB $file -jprot > $basestruc\_jprot.pdb
        perl ../repairPDB $file -seq |tr 'A-Z' 'a-z' > $basestruc.seq
        /opt/SS12-Practical/scwrl4/Scwrl4 -s $basestruc.seq -i $basestruc\_jprot.pdb -o $basestruc\_scrwl.pdb
        perl ../repairPDB $basestruc\_scrwl.pdb -jprot > $basestruc\_forpdb2gromacs.pdb

        /opt/SS12-Practical/gromacs/bin/pdb2gmx -f $basestruc\_forpdb2gromacs.pdb -ff amber03 -water tip3p -o $basestruc\_amber03_forgrompp.gro -p $basestruc\_amber03.top
        /opt/SS12-Practical/gromacs/bin/grompp -v -f 500.mdp -c $basestruc\_amber03_forgrompp.gro -o $basestruc\_amber03.tpr -p $basestruc\_amber03.top
        /opt/SS12-Practical/gromacs/bin/mdrun -v -deffnm  $basestruc\_amber03.tpr

        /opt/SS12-Practical/gromacs/bin/pdb2gmx -f $basestruc\_forpdb2gromacs.pdb -ff charmm27 -water tip3p -o $basestruc\_charmm27_forgrompp.gro -p $basestruc\_charmm27.top
        /opt/SS12-Practical/gromacs/bin/grompp -v -f 500.mdp -c $basestruc\_charmm27_forgrompp.gro -p $basestruc\_charmm27.top -o $basestruc\_charmm27.tpr
        /opt/SS12-Practical/gromacs/bin/mdrun -v -deffnm $basestruc\_charmm27.tpr


        /opt/SS12-Practical/gromacs/bin/pdb2gmx -f $basestruc\_forpdb2gromacs.pdb -ff amber99sb-ildn -water tip3p -o $basestruc\_amber99sb-ildn_forgrompp.gro -p $basestruc\_amber99sb-ildn.top
        /opt/SS12-Practical/gromacs/bin/grompp -v -f 500.mdp -c $basestruc\_amber99sb-ildn_forgrompp.gro -p $basestruc\_amber99sb-ildn.top -o $basestruc\_amber99sb-ildn.tpr
        /opt/SS12-Practical/gromacs/bin/mdrun -v -deffnm $basestruc\_amber99sb-ildn.tpr
done