[gmx-users] %exist hydrogen bond

leila karami karami.leila1 at gmail.com
Tue Feb 22 06:29:36 CET 2011

Dear Justin

My simulation system contains protein, dna and water.
I used your script already for obtaining %exist hydrogen bonds between
protein and dna:


# 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
#   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";
It worked good and output file (summary_Hbmap.dat) was as follows:

#    Donor	          	  Acceptor	            % Exist.
      NGL1	         N	      DT64	        O4	     1.195
      NGL1	         N	      DT82	        O4	     0.797
     ARG57	       NH2	      DA79	       O1P	    19.920
     ARG57	       NH2	      DA80	       O1P	     0.797
     ARG57	       NH2	      DA80	       O2P	    16.335
     ARG57	       NH1	      DA80	       O2P	    43.426

Now I want to use your script for obtaining %exist hydrogen bonds
between protein and water molecules, but output file
(summary_Hbmap.dat) is as follows:

#    Donor	          	  Acceptor	            % Exist.
      NGL1	         N	          	          	     0.160
     ARG58	       NH2	          	          	     0.400
     ARG58	       NH2	          	          	    43.565
     ARG58	       NH1	          	          	     1.839
     ARG58	       NH1	          	          	     0.080
     ARG58	       NH1	          	          	    21.663

What is problem?
Please guide me about that.


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

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