#!/usr/local/bin/perl -w
use strict;
use Fcntl ':flock';
my $file = "inputdata.txt";
open(INFILE, $file) or die "File Not Found: $!";
flock(INFILE, LOCK_EX);
my @students;
while (<INFILE>) {
   push @students, [split / /, $_];
}
my %hash;

# where's $grades coming from?
# $hash{$grades}= $students[0]*0.2 + $student[1]*0.25+$students[2]*0.2
+5 + $student
+s[3]*0.3;

# flock(INFILE, LOCK_UN); # don't use unlock, it's done automagically 
+by close()
close(INFILE);
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update: oops, i forgot 'my @students'

update2: ok, after you updated your code and added input and output, here's my suggestion:

use strict;
use Fcntl ':flock';
my $file = "inputdata.txt";
open(FH, $file) or die "File Not Found: $!";
flock(FH, LOCK_EX);
my @students;
my %hash;
my @mul = (0.2,0.25,0.25,0.3);
while (<FH>) {
  my ($student, @grades) = (split ' ', $_); # split at one or more whi
+tespaces
  my $grade = 0;
  for (0..$#mul) { $grade += $mul[$_] * $grades[$_] }
  $hash{$student} = $grade; # save the sum as a value to the student n
+ame
}
foreach my $key(sort {$hash{$b} <=> $hash{$a}} keys %hash){
  print "$key: $hash{$key}\n";
}
close(INFILE);
[download]

It's not at all obvious from your question what you are aiming for here. This might be something like what your after, though it is limited to calculating grades from just 4 Students as is, but maybe it will get you started. It would be fairly easy to extend this to deal with any number of students or scores, but I couldn't see any pattern in how you are deriving your constant factors.

#! perl -slw
use strict;

# do open and lock stuff
my @students = map{ [ split ] } <DATA>;

print "Student scores\n------------";
print "@$_" for @students;

my %grades;
for my $grade ( 0 .. 2 ) {
    $grades{ $grade } 
        = $students[ 0 ][ $grade ] * 0.2
        + $students[ 1 ][ $grade ] * 0.25
        + $students[ 2 ][ $grade ] * 0.25
        + $students[ 3 ][ $grade ] * 0.3
}
print "\nGrades\n--------";
print "$_ => $grades{ $_ }" for sort keys %grades;


=Output
P:\test>337154
Student scores
------------
1 2 3
2 1 3
3 1 2
3 2 1

Grades
--------
0 => 2.35
1 => 1.5
2 => 2.15
=cut

__DATA__
1 2 3
2 1 3 
3 1 2
3 2 1
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Here's my take. Modifiying it to read input from a file or for pretty printing is left as an exercise.

#!/usr/bin/perl

use Data::Dumper;

my @students = qw {
  Thomas 60 10 20 85
  Samuel 35 90 80 65
  Adam   100 90 85 52
};

my %h;
while ( my ($student, @vals) = splice @students, 0, 5) {
  $h{$student} +=  @vals[$_] * (0.2, 0.25, 0.25, 0.3)[$_] for 0..3;
}

print Dumper \%h;
[download]

Regarding the code provided by you: one hint - split / / is not probably what you want. Try split // (and see perldoc -f split). Another hint - there are at least three more obvious logical mistakes (...hash keys(mental confusion)...two issues with contents of @students (forgot about references, extra element, again confusion)...) .