View source for 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`;

}
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