#!/usr/bin/perl -w

$dir = "/net/klab2/u2/home/fmohammad/GFP2/run1";

opendir (DIR, $dir) or die $!;
@one = readdir (DIR);

foreach $file (@one)
{

        $initialfile2 = "$file";

        open FILETWO, "$initialfile2" or die "cannot open $initialfile2 for read\n";
        while ($line2 = <FILETWO>)
        {
        chomp $line2;

        @one=split(/\s+/, $line2);

                if ($one[0]=~m/^HETATM/)
                {
                        if ($one[2]eq "C4")
                        {
                        $xC4=$one[6];
                        $yC4=$one[7];
                        $zC4=$one[8];
                        }

                        if ($one[2]eq "C1")
                        {
                        $xC1=$one[6];
                        $yC1=$one[7];
                        $zC1=$one[8];
                        }

                        if ($one[2]eq "C13")
                        {
                        $xC13=$one[6];
                        $yC13=$one[7];
                        $zC13=$one[8];
                        }
                }
        }
        close FILETWO;

        $initialfile = "1GFL.pdb";
        open FILEONE, "$initialfile" or die "cannot open $initialfile for read\n";
        while ($line = <FILEONE>)
        {
        chomp $line;

        @two=split(/\s+/, $line);

                if ($two[0]=~m/^ATOM/)
                {
                        if ($two[1]eq "479")
                        {
                        $xS=$two[6];
                        $yS=$two[7];
                        $zS=$two[8];
                        }

                        if ($two[1]eq "484")
                        {
                        $xY=$two[6];
                        $yY=$two[7];
                        $zY=$two[8];
                        }

                        if ($two[1]eq "496")
                        {
                        $xG=$two[6];
                        $yG=$two[7];
                        $zG=$two[8];
                        }
                }
        }
        close FILEONE;

        $part1 = ((($xC1 - $xS)**2) + (($yC1 - $yS)**2) + (($zC1 - $zS)**2));
        $part2 = ((($xC4 - $xY)**2) + (($yC4 - $yY)**2) + (($zC4 - $zY)**2));
        $part3 = ((($xC13 - $xG)**2) + (($yC13 - $yG)**2) + (($zC13 - $zG)**2));
        $sum = $part1 + $part2 + $part3;
        $sum1 = $sum / 3;
        $rmsd = sqrt ($sum1);
        print"$rmsd\n";
}

##</code><code>##

Use of uninitialized value $xC1 in subtraction (-) at getrmsd2.pl line 80.
Use of uninitialized value $yC1 in subtraction (-) at getrmsd2.pl line 80.
Use of uninitialized value $zC1 in subtraction (-) at getrmsd2.pl line 80.
Use of uninitialized value $xC4 in subtraction (-) at getrmsd2.pl line 81.
Use of uninitialized value $yC4 in subtraction (-) at getrmsd2.pl line 81.
Use of uninitialized value $zC4 in subtraction (-) at getrmsd2.pl line 81.
Use of uninitialized value $xC13 in subtraction (-) at getrmsd2.pl line 82.
Use of uninitialized value $yC13 in subtraction (-) at getrmsd2.pl line 82.
Use of uninitialized value $zC13 in subtraction (-) at getrmsd2.pl line 82.
70.8509364158301
Use of uninitialized value $xC1 in subtraction (-) at getrmsd2.pl line 80.
Use of uninitialized value $yC1 in subtraction (-) at getrmsd2.pl line 80.
Use of uninitialized value $zC1 in subtraction (-) at getrmsd2.pl line 80.
Use of uninitialized value $xC4 in subtraction (-) at getrmsd2.pl line 81.
Use of uninitialized value $yC4 in subtraction (-) at getrmsd2.pl line 81.
Use of uninitialized value $zC4 in subtraction (-) at getrmsd2.pl line 81.
Use of uninitialized value $xC13 in subtraction (-) at getrmsd2.pl line 82.
Use of uninitialized value $yC13 in subtraction (-) at getrmsd2.pl line 82.
Use of uninitialized value $zC13 in subtraction (-) at getrmsd2.pl line 82.
70.8509364158301
1.68309110468408