MutEn.pl

1. !/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";

1. 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";

1. 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";

1. 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";

1. 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";

1. Run minimization with Gromacs:

print "\tRuning PDB2GMX\n";

1. PDB2GMX

`pdb2gmx -f ${id}_NoSolNoH.pdb -o ${id}.gro -p ${id}.top -water tip3p -ff amber03`;

print "\tCreating MDP file\n";

1. 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";

1. GROMPP

`grompp -v -f Minimize.mdp -c ${id}.gro -p ${id}.top -o ${id}.tpr`;

print "\tRuning MDRUN\n";

1. MDRUN

`mdrun -v -deffnm ${id}`;

print "\tAnalyzing\n\n\n\n";

1. Analyze

`g_energy -f ${id}.edr -o ${id}_Energy.xvg`;

}