Poojari, Chetan wrote:
Hello Justin,
I deleted the original file and re ran the script. I did get the output as such:
# Donor Acceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
.
.
.
But in the second line of the output theres no donor or acceptor but still i
gives 0.040 % existence number. I scrolled down to end of the output file to
check if incase the %exist. is missing for the last atom.......but everything
seems to be fine.
Please can i know why is it showing this number.
I have no idea. There is some mismatch between the lines of the .xpm file and
the .ndx file, or for some reason the numbers in the .ndx file cannot be mapped
back onto the .pdb file. It could mean that this particular hydrogen bond is
undefined for those reasons, or something else later in the output file (since
the .xpm file is read "backward," so to speak) has caused a problem and shifted
the indices.
If you send me your input files (off-list), I will try to find out what's going
on with them. No promises, but I'll try to find some time.
-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 22:48
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out line 151 and braces enclosing it.
# 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, $resnum);
}
}
# }
Following is the ouput:
In the beginning of the file i had these :
# Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU11 OE1 0.020
GLU11 OE2 0.020
HIS13 O 0.040
GLN15 OE1 0.040
Following these i had below lines., in the same file:
# Donor Acceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
ASP1 N SOL177 OW 0.020
ASP1 N SOL179 OW 0.020
.
.
.
.
SOL682 OW HIS13 O 0.020
SOL682 OW GLN15 OE1 0.020
SOL682 OW GLN15 NE2 0.040
SOL682 OW ALA21 O 0.020
SOL682 OW GLU22 OE1 0.140
Delete the original file and run the script again. The output is simply
appended if the same file is already present. Or, modify the output routines.
The latter part of the file is the expected output.
-Justin
Kind regards,
chetan.
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: 13 December 2010 19:54
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
Hello Justin,
I commented out the lines from 151-161
# unless ($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.
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
