[gmx-users] %exist hydrogen bond

[Justin A. Lemkul]

leila karami wrote:
> 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.
> 

The script explicitly excludes water.  Comment out the "unless" statement on or 
around line 151 and the enclosing brace on line 161 (but leave the intervening 
content alone).

-Justin

> 
> 
> 
> 
> 

-- 
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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

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