[gmx-users] %exist hydrogen bond

[leila karami]

Dear Justin

thanks for your reply.

I did what you said as follows:

your main script=

# Open up the structure file and work with it
print "Processing coordinate file...\n";
foreach $_ (@coord) {
     my @line = split(" ", $_);
     my $natom = $line[1];
     my $name = $line[2];
     my $resn = $line[3];
     my $resnum = $line[4];
151
152     if ($line[0] =~ /ATOM/) {
153         unless ($resn =~ /SOL/) {
154             for (my $z=1; $z<=$nres; $z++) {
155                 if ($donors{$z} == $natom) {
156                     $donor_names[$z] = $name;
157                     $donor_resn[$z] = join('', $resn, $resnum);
158                 } elsif ($acceptors{$z} == $natom) {
159                     $acceptor_names[$z] = $name;
160                     $acceptor_resn[$z] = join('', $resn, $resnum);
161              }
             }
         }
     }
}

# open a single output file for writing


my modified script=

# Open up the structure file and work with it
print "Processing coordinate file...\n";
foreach $_ (@coord) {
     my @line = split(" ", $_);
     my $natom = $line[1];
     my $name = $line[2];
     my $resn = $line[3];
     my $resnum = $line[4];

     if ($line[0] =~ /ATOM/) {
                      for (my $z=1; $z<=$nres; $z++) {
                 if ($donors{$z} == $natom) {
                     $donor_names[$z] = $name;
                     $donor_resn[$z] = join('', $resn, $resnum);
                 } elsif ($acceptors{$z} == $natom) {
                     $acceptor_names[$z] = $name;
                     $acceptor_resn[$z] = join('', $resn, $resnum);
                }
         }
     }
}

# open a single output file for writing

is my manner true?
when I used modified script, problem was not solved. and output file is as
follows:

#    Donor                    Acceptor                % Exist.
                                                             0.160
      NGL1             N                                        0.400
     ARG58           NH2                                    43.565
     ARG58           NH2                                     1.839
     ARG58           NH1                                     0.080
     ARG58           NH1                                     21.663
     ARG58           NH1                                     0.160
     ARG58            NE                                      1.359
.
.
.
.
                                          GLY3             O         1.759
                                          GLY4             O         0.400
                                         THR47             O        61.711
                                         ASN51           OD1        16.867
                                         ASN51           ND2         0.320
                                        GLN23           OE1        11.191
.
.
.

how to fix it?
-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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