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
--
========================================
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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