[gmx-users] HBOND probability
Poojari, Chetan
c.poojari at fz-juelich.de
Mon Dec 13 22:45:23 CET 2010
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, $resnum);
}
}
# }
Following is the ouput:
In the beginning of the file i had these :
# Donor Acceptor % Exist.
0.040
ASP1 N 0.020
ASP1 N 0.020
ASP1 N 0.100
GLU11 OE1 0.020
GLU11 OE2 0.020
HIS13 O 0.040
GLN15 OE1 0.040
Following these i had below lines., in the same file:
# Donor Acceptor % Exist.
0.040
ASP1 N SOL171 OW 0.020
ASP1 N SOL172 OW 0.020
ASP1 N SOL175 OW 0.100
ASP1 N SOL177 OW 0.020
ASP1 N SOL179 OW 0.020
.
.
.
.
SOL682 OW HIS13 O 0.020
SOL682 OW GLN15 OE1 0.020
SOL682 OW GLN15 NE2 0.040
SOL682 OW ALA21 O 0.020
SOL682 OW GLU22 OE1 0.140
Kind regards,
chetan.
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 13 December 2010 19:54
To: Gromacs Users' List
Subject: Re: [gmx-users] HBOND probability
Poojari, Chetan wrote:
> Hello Justin,
>
> I commented out the lines from 151-161
>
> # unless ($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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at 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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at 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!
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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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