I hard-coded the input file names for my own convenience while testing.

somewhat optimised - I like to think of it as a good mix between obvious and efficient.

 #!/usr/bin/perl -w

use strict;

my @solvents;
my @structs;

my @fields = qw(atom number name resname resnumber xpos ypos zpos q ra
+dius);

slurp_file(\@solvents, "solv.txt");
slurp_file(\@structs,  "struct.txt");

print "Atoms in solvent file is ",   scalar(@solvents), "\n";
print "Atoms in structure file is ", scalar(@structs),  "\n";

my @desBooli = map {0} @solvents; # could be done other ways

open(test2, ">OverL.txt")
  or die ("Couldn't open file OverL.txt :: $!\n");

for (my $i = 0; $i < @solvents; $i++) {
  for (my $j = 0; $j < @structs; $j++) {
    # I am sure there is a better way
    my $dist = sqrt(($solvents[$i]->{xpos} - $structs[$j]->{xpos})**2+
                    ($solvents[$i]->{ypos} - $structs[$j]->{ypos})**2+
                    ($solvents[$i]->{zpos} - $structs[$j]->{zpos})**2)
+;
    my $radSum = $solvents[$i]->{radius} + $structs[$j]->{radius};
    if($dist < $radSum) {
      print test2 "$i - Overlap for atoms solvent $solvents[$i]->{resn
+umber} and structure $structs[$j]->{resnumber}\n";
      $desBooli[$i] = 1;
    }
  }
}
close test2;

open(test1, ">Solvent.pdb")
  or die ("Couldn't open file Solvent.pdb :: $!\n");
for (my $i = 0; $i < @solvents; $i++) {
    if ($desBooli[$i] == 0){ # no overlap
       print test1 dump_solvent($solvents[$i]), "\n";
    }
}
close test1;

exit;

sub slurp_file {
  my ($array, $name) = @_;

  open(FILE, $name) or die ("Couldn't open file $name:: $!\n");
  while (<FILE>) {
    chomp; # trim line endings
    next if /^\s*$/; # strip blank lines
    my %hash = ();
    @hash{@fields} = split /\s+/; # hash slice
    push @{$array}, \%hash;
  }
  use Data::Dumper;
  close FILE;
}

sub dump_solvent {
  my ($solvent) = @_;

  join ' ', @{$solvent}{@fields};
}
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