Poojari, Chetan wrote:
Hello Justin,
I commented out the lines from 151-161
# unless ($resn =~ /SOL/) {
# for (my $z=1; $z<=$nres; $z++) {
# if ($donors{$z} == $natom) {
# $donor_names[$z] = $name;
# $donor_resn[$z] = join('', $resn, $resnum);
# } elsif ($acceptors{$z} == $natom) {
# $acceptor_names[$z] = $name;
# $acceptor_resn[$z] = join('', $resn, $resnum);
# }
# }
# }
I am ending up with the similar output.
Please comment out *just* the unless line (151) and the brace that encloses it,
not the entire section. Otherwise, I suspect that nothing actually happened.
That's the entire pattern matching operation there. Without it, the script
probably doesn't do anything at all.
-Justin
Kind regards,
chetan.
_______________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:06
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
As suggested i did remove the chain identifiers, so i do get residue numbers in
my output. But the end result is still the same.
While choosing 2 groups to create index file, i choose protein as my first
group and sol as my second group. (I choose the entire protein and solvent
group as I wanted to know the protein residues involved in hydrogen bonding
with the water molecules over time)
This is how my index file looks which is generated from g_hbond. (retained
only hbonds....)
[ hbonds_Protein-SOL ]
1 2 7094
1 2 7097
1 2 7106
1 2 7112
.
.
7088 7089 8
7088 7089 9
7088 7089 24
7088 7089 67
7088 7089 73
7088 7089 84
Summary.dat file contains:
Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU3 OE2 0.020
ARG5 O 0.020
HIS6 NE2 0.020
Please can i know what might be the problem here??
The script does not process hydrogen bonds involving SOL. The reason is that
the atom numbering goes haywire if you have too many waters and the output
doesn't make sense any more.
If you need to analyze anything involving SOL, just take out the "unless"
statement on (or around) line 151 and the closing brace a few lines later. I
haven't tested that, but it should be the only thing keeping SOL from being
considered.
-Justin
Kind regards,
chetan
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I wanted to find the probability of hydrogen bond formed between my peptide and
water molecules over time. So I used your plot_hbmap.pl script.
As mentioned in the script file, my index file contained atom numbers only from
the [hbonds...] section, rest were deleted.
Heres my short output after running the script:
# Donor Acceptor % Exist.
0.004
ALAA N 0.004
ALAA N 0.016
ALAA N 0.012
ALAA N 0.008
ALAA O 0.008
ASNA OD1 0.012
GLYA O 0.008
ALAA O 0.008
Please can I know if this is the expected output from the script ??? if not
please can I know what might be wrong in my input ????
This is absolutely not the correct output. Probably your index file is not
correct. Also note that if you want proper residue names/numbers, you need to
use a .pdb file that does not have chain identifiers.
-Justin
Kind regards,
chetan.
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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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========================================
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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www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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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