Hi all, I was wondering if you could find the reason for this issue in the code posted below?

I am trying to automate the way I use a program (Gromacs) and edit its outputs. So first I loop through my molecules and issue the Gromacs command (g_angle) which works fine. Then I commented the g_angle command out to test the rest of the script. What I want to do now is open (for reading) the output of the previously used command, to manipulate it and write another file.

However the line open $input, '<', '/Users/athina/check-ma/$ID${l}/F${j}\/gangle-dihedrals-${i}${id}${k}.xvg' or die $!; fails as "no such file or directory" but the file exists.

The line print  `ls /Users/athina/check-ma/$ID${l}/F${j}\/gangle-dihedrals-${i}${id}${k}.xvg`; that I've used as a test works fine and returns the file.

What is happening? :( Thank you so much for your time!

 #!/usr/bin/perl

use warnings;
use strict;

my $id = "ac";
my $ID = "AC";
my $g_angle = "/usr/local/gromacs/bin/g_angle";
my $i;
my $k;

my $input;
my $output;

#disable Gromacs backups because otherwise it fails after writing 99x 
+copies
  if(!defined $ENV{GMX_MAXBACKUP}) {
    $ENV{GMX_MAXBACKUP}=-1
  }

for ($i=2; $i<=2; $i++) {
my $j = sprintf ("%05d", $i);

  for ($k=15; $k<=15; $k++) {
  my $l = sprintf ("%04d", $k);
  my $path = "/Users/athina/check-ma/$ID${l}/F${j}";
  my $dashFolder = "/media/data/athina/dash-test/$ID${l}";

   #`$g_angle -f $path\/${i}${id}${k}.mdsol.centered.xtc -n /Users/ath
+ina/check-ma/$ID${l}/F00001/dihedrals-1${id}${k}.ndx -type dihedral -
+all -ov $path\/gangle-dihedrals-${i}${id}${k}.xvg -od $path\/out.xvg`
+;

print  `ls /Users/athina/check-ma/$ID${l}/F${j}\/gangle-dihedrals-${i}
+${id}${k}.xvg`;

   open $input, '<', '/Users/athina/check-ma/$ID${l}/F${j}\/gangle-dih
+edrals-${i}${id}${k}.xvg' or die $!;
   open $output, '>', '/Users/athina/check-ma/$ID${l}/F${j}\/in-dihedr
+als-${i}${id}${k}.txt' or die $!;
  
    while (my $line = <$input>) {

    chomp $line;            # remove end-of-line character
    $line =~ s/^\s+//;       # strip leading whitespace
    next unless $line;      # skip blank lines

    # skip first 12 lines
    next unless $. > 12;     # $. contains current line number

    my @columns = split(/\s+/, $line);    # split columns on whitespac
+e

    my $col1 = shift @columns;  # column 1 (throw away)
    my $col2 = shift @columns;  # column 2 (throw away)
    my $col3 = shift @columns;  # column 3 (special - keep this one)
    my $result = sprintf("%8.3f", $col3); # special format for col 3

     # loop over remaining columns, appending to result string 
     for my $c (@columns) {
     my $data = sprintf("%9.3f", $c);
     $result .= " $data";
     }

    print $output "$result\n";
    
    } ###
  } ### for k loop
} ### for i loop

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In reply to 'open for read' fails as "no such file or directory" but file is there by fasoli

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