Match the values you want with a regex

#!perl
use strict;

my @tpr = qw(
AC0001_F00001_S00011.tpr 
AC0001_F00002_S00012.tpr 
AC0001_F00003_S00013.tpr
AC0002_F00001_S00021.tpr 
AC0002_F00002_S00022.tpr 
AC0002_F00003_S00023.tpr
AC0003_F00001_S00031.tpr 
AC0003_F00002_S00032.tpr 
AC0003_F00003_S00033.tpr);
             
foreach (@tpr) {
   
  if (/(\w{2})(\d{4})_F(\d{5})_S(\d{5})/){

    my $id = "AC";
    my $molec  = $2;
    my $frame  = $3;
    my $mdstep = $4;

    # molecule 1 to 2 and frame 1 to 2
    if ( ($molec =~ /000[12]/) && ($frame =~ /0000[12]/) ){ 
      print "$_\n";
    }
  } 
  
} # end of loop through tpr files
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