[gmx-users] %exist hydrogen bond

[leila karami]

Dear Justin

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

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

#    Donor	          	  Acceptor	            % Exist.
          	          	          	          	     0.000
      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