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
--
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