[gmx-users] Percentage of H-bonds

[Carla Jamous]

Thank you Justin,

you Perl script has been a great help!

Cheers,
Carla

On Mon, Oct 11, 2010 at 4:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> I wrote a Perl script to do a similar task (appended below).  Perhaps it
> will be useful to you.  I hope it works; I had to hack out some things that
> were specific to my needs and have done only limited testing.
>
> -Justin
>
>
>
> #!/usr/bin/perl
>
> #
> # plot_hbmap.pl - plot the probability of finding a particular hydrogen
> bond
> # based on several input files:
> #   1. coordinate file (for atom naming) - MUST be a .pdb file with NO
> CHAIN IDENTIFIERS
> #   2. hbmap.xpm
> #   3. hbond.ndx (modified to contain only the atom numbers in the
> [hbonds...] section, nothing else)
> #
>
> use strict;
>
> unless(@ARGV) {
>    die "Usage: perl $0 -s structure.pdb -map hbmap.xpm -index hbond.ndx\n";
> }
>
> # define input hash
> my %args = @ARGV;
>
> # input variables
> my $map_in;
> my $struct;
> my $ndx;
>
> if (exists($args{"-map"})) {
>    $map_in = $args{"-map"};
> } else {
>    die "No -map specified!\n";
> }
>
> if (exists($args{"-s"})) {
>    $struct = $args{"-s"};
> } else {
>    die "No -s specified!\n";
> }
>
> if (exists($args{"-index"})) {
>    $ndx = $args{"-index"};
> } else {
>    die "No -index specified!\n";
> }
>
> # open the input
> open(MAP, "<$map_in") || die "Cannot open input map file!\n";
> my @map = <MAP>;
> close(MAP);
>
> open(STRUCT, "<$struct") || die "Cannot open input coordinate file!\n";
> my @coord = <STRUCT>;
> close(STRUCT);
>
> open(NDX, "<$ndx") || die "Cannot open input index file!\n";
> my @index = <NDX>;
> close(NDX);
>
> # determine number of HB indices and frames
> my $nres = 0;
> my $nframes = 0;
> for (my $i=0; $i<scalar(@map); $i++) {
>    if ($map[$i] =~ /static char/) {
>        my $res_line = $map[$i+1];
>        my @info = split(" ", $res_line);
>
>        $nframes = $info[0];
>        my @nframes = split('', $nframes);
>        shift(@nframes);    # get rid of the "
>        $nframes = join('', @nframes);
>
>        $nres = $info[1];
>    }
> }
>
> print "Processing the map file...\n";
> print "There are $nres HB indices.\n";
> print "There are $nframes frames.\n";
>
> # initialize hashes for later output writing
> # counter $a holds the HB index from hbond.ndx
> my %hbonds;
> for (my $a=0; $a<$nres; $a++) {
>    $hbonds{$a+1} = 0;
> }
>
> # donor/acceptor hashes for bookkeeping purposes
> my %donors;
> for (my $b=1; $b<=$nres; $b++) {
>    $donors{$b} = 0;
> }
>
> my %acceptors;
> for (my $c=1; $c<=$nres; $c++) {
>    $acceptors{$c} = 0;
> }
>
> # clean up the output - up to 18 lines of comments, etc.
> splice(@map, 0, 18);
>
> # remove any "x-axis" or "y-axis" lines
> for (my $n=0; $n<scalar(@map); $n++) {
>    if (($map[$n] =~ /x-axis/) || ($map[$n] =~ /y-axis/)) {
>            shift(@map);
>            $n--;
>    }
> }
>
> # There should now be $nres lines left in the file
> # The HB map for the last index is written first (top-down in .xpm file)
> #   * Element 0 is index $nres, element 1 is $nres-1, etc.
>
> for (my $i=$nres; $i>=1; $i--) {
>    # There will be $nframes+2 elements in @line (extra two are " at
> beginning
>    # and end of the line)
>    # Establish a conversion factor and split the input lines
>    my $j = $nres - $i;
>    my @line = split('', $map[$j]);
>
>    # for each index, write to hash
>    for (my $k=1; $k<=($nframes+1); $k++) {
>        if ($line[$k] =~ /o/) {
>            $hbonds{$i}++;
>        }
>    }
> }
>
> print "Processing the index file...\n";
>
> # Open up the index file and work with it
> for (my $n=0; $n<$nres; $n++) {
>    my @line = split(" ", $index[$n]);
>    $donors{$n+1} = $line[0];
>    $acceptors{$n+1} = $line[2];
> }
>
>
> # some arrays for donor and acceptor atom names
> my @donor_names;
> my @donor_resn;
> my @acceptor_names;
> my @acceptor_resn;
>
> # 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/) {
>        unless ($resn =~ /SOL/) {
>            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
> open(OUT, ">>summary_HBmap.dat") || die "Cannot open output file!\n";
> printf(OUT "%10s\t%10s\t%10s\t%10s\%10s\n", "#    Donor", " ", "Acceptor",
> " ", "% Exist.");
>
> for (my $o=1; $o<=$nres; $o++) {
>    printf(OUT "%10s\t%10s\t%10s\t%10s\t%10.3f\n", $donor_resn[$o],
> $donor_names[$o], $acceptor_resn[$o], $acceptor_names[$o],
> (($hbonds{$o}/$nframes)*100));
> }
>
> close(OUT);
>
> exit;
>
>
>
>
> Carla Jamous wrote:
>
>> Hi everyone,
>>
>> I tried to analyze the H-bonds in my trajectory with g-hbond and I
>> analysed the xpm and ndx file. But now I need to know the percentage of
>> existence of each hbond during my trajectory. Is there a way to do it with a
>> command line? Or is there a program (someone told me there are python
>> programs for analysis of gromacs trajectories) to extract this information
>> from the .xpm file?
>>
>> Thank you.
>>
>> Cheers,
>> Carla
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101014/cd0fa1b8/attachment.html>