MutEn.pl

#!/usr/bin/perl -w my $PDB='2FBT'; # Insert PDB code for protein my @fileslist = <${PDB}_*>; # Create an array with all the mutant structures. foreach my $file ( @fileslist ) { print "--> FILE ${file}\n\n\n"; print "Creating ID from file name\n\n"; # Create ID from file name my @fullname = split(/.pdb/, $file); # Splits the file name in two parts. my $id = $fullname[0]; # Identifier of file name is the first part (before ".pdb"). print "Creating sequence file as an input for SCWRL\n\n"; # Creates sequence file as an input for SCWRL: # Extract sequence from PDB file: `repairPDB ${id}.pdb -seq >> ${id}.fasta`; # Creates sequence file. # It is now necessary to convert the sequence to lower case: # Start open(SEQ, "<${id}.fasta"); # Opens the sequence file. open(SEQLC, ">${id}_LC.fasta"); # Opens a new file to store the lower case sequence. my $sequence=<SEQ>; # Stores the sequence in a string. my $sequencelc = lc($sequence); # Converts the sequence to lower case. print SEQLC $sequencelc; # Prints the lower case sequence string to file. close SEQ; close SEQLC; # End print "Runing SCWRL to assert the position of side-chains\n\n"; # Runs SCWRL to assert the position of side-chains: `scwrl -s ${id}_LC.fasta -i ${id}.pdb -o ${id}_Scwrl.pdb`; print "Remove Solvent molecules and Hydrogen atoms to prepare the structure for energy minimization\n\n"; # Remove Solvent molecules and Hydrogen atoms to prepare the structure for energy minimization: `repairPDB ${id}_Scwrl.pdb -nosol -noh >> ${id}_NoSolNoH.pdb`; # Removes Water molecules and Hydrogen atoms from structure. print "Runing minimization with Gromacs\n"; # Run minimization with Gromacs: print "\tRuning PDB2GMX\n"; # PDB2GMX `pdb2gmx -f ${id}_NoSolNoH.pdb -o ${id}.gro -p ${id}.top -water tip3p -ff amber03`; print "\tCreating MDP file\n"; # Create MDP file: open(MDP,">Minimize.mdp"); print MDP "title = PBSA minimization in vacuum\n"; print MDP "cpp = /usr/bin/cpp\n"; print MDP "define = -DFLEXIBLE -DPOSRES\n"; print MDP "implicit_solvent = GBSA\n"; print MDP "integrator = steep\n"; print MDP "emtol = 1.0\n"; print MDP "nsteps = 500\n"; print MDP "nstenergy = 1\n"; print MDP "energygrps = System\n"; print MDP "ns_type = grid\n"; print MDP "coulombtype = cut-off\n"; print MDP "rcoulomb = 1.0\n"; print MDP "rvdw = 1.0\n"; print MDP "constraints = none\n"; print MDP "pbc = no"; close MDP; print "\tRuning GROMPP\n"; # GROMPP `grompp -v -f Minimize.mdp -c ${id}.gro -p ${id}.top -o ${id}.tpr`; print "\tRuning MDRUN\n"; # MDRUN `mdrun -v -deffnm ${id}`; print "\tAnalyzing\n\n\n\n"; # Analyze `g_energy -f ${id}.edr -o ${id}_Energy.xvg`; }