#!/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 $initialfile
+2 for read\n";
while ($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";
}
and here is the error:
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 lin
+e 82.
Use of uninitialized value $yC13 in subtraction () at getrmsd2.pl lin
+e 82.
Use of uninitialized value $zC13 in subtraction () at getrmsd2.pl lin
+e 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 lin
+e 82.
Use of uninitialized value $yC13 in subtraction () at getrmsd2.pl lin
+e 82.
Use of uninitialized value $zC13 in subtraction () at getrmsd2.pl lin
+e 82.
70.8509364158301
1.68309110468408
