I have never looked at a PDB before but I am referring http://www.wwpdb.org/documentation/format32/sect9.html for it. Also assuming (from the above write ups) that you are looking to exclude lines with '\sH\s\s' (when it starts with ATOM) and '\sHOH' (when it starts with HETATM).
It can be done with following 2 regexs 
/ATOM  .{6} H  /
/HETATM.{6} HOH/

[download]
or it can be joined in as shown below 
use strict;

while (<DATA>) {
    my $data = $_;
    print $data 
        if ($data !~ /(?:ATOM  .{6} H  )|(?:HETATM.{6} HOH)/);
}

__DATA__
ATOM    601  H   LEU A  75     -17.070 -16.002   2.409  1.00 55.63    
+       N  
ATOM    602  CA  LEU A  75     -16.343 -16.746   3.444  1.00 55.50    
+       C  
ATOM    603  C   LEU A  75     -16.499 -18.263   3.300  1.00 55.55    
+       C  
ATOM    604  H   LEU A  75     -16.645 -18.789   2.195  1.00 55.50    
+       O  
ATOM    605  CB  LEU A  75     -16.776 -16.283   4.844  1.00 55.51    
+       C  
TER     606      LEU A  75   
ATOM   1185  O   LEU B  75      26.292  -4.310  16.940  1.00 55.45    
+       O  
ATOM   1186  CB  LEU B  75      23.881  -1.551  16.797  1.00 55.32    
+       C  
TER    1187      LEU B  75                                            
+          
HETATM 1188  HOH SRT A1076     -17.263  11.260  28.634  1.00 59.62    
+       H  
HETATM 1189  HA  SRT A1076     -19.347  11.519  28.341  1.00 59.42    
+       H  
HETATM 1190  H3  SRT A1076     -17.157  14.303  28.677  1.00 58.00    
+       H  
HETATM 1191  HOH SRT A1076     -15.110  13.610  28.816  1.00 57.77    
+       H  
HETATM 1192  O1  SRT A1076     -17.028  11.281  31.131  1.00 62.63    
+       O  
ATOM    295  HB2 ALA A  18       4.601  -9.393   7.275  1.00  0.00    
+       H  
ATOM    296  HB3 ALA A  18       3.340  -9.147   6.043  1.00  0.00    
+       H  
TER     297      ALA A  18

[download]
Refer below the output 
# Output
# ATOM    602  CA  LEU A  75     -16.343 -16.746   3.444  1.00 55.50  
+         C  
# ATOM    603  C   LEU A  75     -16.499 -18.263   3.300  1.00 55.55  
+         C  
# ATOM    605  CB  LEU A  75     -16.776 -16.283   4.844  1.00 55.51  
+         C  
# TER     606      LEU A  75   
# ATOM   1185  O   LEU B  75      26.292  -4.310  16.940  1.00 55.45  
+         O  
# ATOM   1186  CB  LEU B  75      23.881  -1.551  16.797  1.00 55.32  
+         C  
# TER    1187      LEU B  75                                          
+            
# HETATM 1189  HA  SRT A1076     -19.347  11.519  28.341  1.00 59.42  
+         H  
# HETATM 1190  H3  SRT A1076     -17.157  14.303  28.677  1.00 58.00  
+         H  
# HETATM 1192  O1  SRT A1076     -17.028  11.281  31.131  1.00 62.63  
+         O  
# ATOM    295  HB2 ALA A  18       4.601  -9.393   7.275  1.00  0.00  
+         H  
# ATOM    296  HB3 ALA A  18       3.340  -9.147   6.043  1.00  0.00  
+         H  
# TER     297      ALA A  18

[download]

In reply to Re: Help for a regex problem ? by ashish.kvarma
in thread Help for a regex problem ? by hellworld

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