I don't see anything specifically wrong with line 58 and the final for loop. However I did find a serious typo, in your code to find the distance between the two atoms, you accidentally used the Z co-ordinate twice instead of Y. I'm not able to help you optimize the algorithm, but I did clean up the code so it is much more readable (and runs under strict). Allthough I did use 'constant' so all of the caveats for it apply. Be careful of PM wrapping this code. Oh and since you only provided one example line I tested this against some randomly generated data which may not have been correct :).

#!/usr/bin/perl -w
use strict;

use constant {
            RAD => 9,
            X => 5,
            Y => 6,
            Z => 7,
            NB => 1,
            REST => 10,
};

my $file;
print "Please type the filename with the solvent: ";
chomp($file = <STDIN>);
die "File \"$file\" doesn\'t seem to exist!!\n" unless -e $file;
open(SOLVFILE, $file) or die("Couldn't open file  $file\n");

print "Please type the filename with the structure: \n";
chomp($file = <STDIN>);
die "File \"$file\" doesn\'t seem to exist!!\n" unless -e $file;
open(STRUCTFILE, $file) or die("Couldn't open file  $file\n");

open(PDB, ">Solvent.pdb") or die "$!";
open(OVERL, ">OverL.txt") or die "$!";

my @solv;
my $line;
while ($line=<SOLVFILE>)
{
    chomp $line;
    push @solv, [split /\s+/, $line];
    push @{$solv[-1]}, $line;
}
close SOLVFILE;
print "Number of atoms in solvent file is ",$#solv+1," \n";

my @struct;
while ($line=<STRUCTFILE>)
{
    chomp($line);
    push @struct, [split /\s+/, $line];
    push @{$struct[-1]}, $line;
}
close STRUCTFILE;
print "Number of atoms in structure file is ",$#struct+1," \n";

for (my $i = 0; $i <= $#solv; $i++)
{
    my $v = $solv[$i];
    for my $t (@struct)
    {
        
        if (    # Sum of radius is greater than distance
                # between the atoms
            ($v->[RAD] + $t->[RAD])
            > 
            sqrt(
              ($v->[X] - $t->[X])**2
            + ($v->[Y] - $t->[Y])**2
            + ($v->[Z] - $t->[Z])**2
            ))
        {
            print OVERL "Overlap for atoms ",
                   $v->[NB]," and ",$t->[NB],"\n";
        } else {
                print PDB $v->[REST],"\n";
        }
    }
}
close OVERL;
close PDB;
exit;
[download]

HTH

tedrek

Update: I realized the whole @overlap functionality could be moved into the main loop, so I did :). Also you could change the outer for loop to to a while(<SOLV>) and not need to read SOLV into memory.

Update2: After seeing graff's code I realized the print to PDB was supposed to be in a else block.

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