[gmx-users] HBOND probability
Justin A. Lemkul
jalemkul at vt.edu
Tue Dec 14 14:25:55 CET 2010
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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at 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, $resnum);
>> }
>> }
>> # }
>>
>>
>> Following is the ouput:
>>
>> In the beginning of the file i had these :
>>
>> # Donor Acceptor % Exist.
>> 0.040
>> ASP1 N 0.020
>> ASP1 N 0.020
>> ASP1 N 0.100
>>
>> GLU11 OE1 0.020
>> GLU11 OE2 0.020
>> HIS13 O 0.040
>> GLN15 OE1 0.040
>>
>>
>> Following these i had below lines., in the same file:
>>
>> # Donor Acceptor % Exist.
>> 0.040
>> ASP1 N SOL171 OW 0.020
>> ASP1 N SOL172 OW 0.020
>> ASP1 N SOL175 OW 0.100
>> ASP1 N SOL177 OW 0.020
>> ASP1 N SOL179 OW 0.020
>> .
>> .
>> .
>> .
>> SOL682 OW HIS13 O 0.020
>> SOL682 OW GLN15 OE1 0.020
>> SOL682 OW GLN15 NE2 0.040
>> SOL682 OW ALA21 O 0.020
>> SOL682 OW GLU22 OE1 0.140
>>
>>
>
> Delete the original file and run the script again. The output is simply
> appended if the same file is already present. Or, modify the output routines.
> The latter part of the file is the expected output.
>
> -Justin
>
>> Kind regards,
>> chetan.
>>
>>
>>
>>
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
>> Sent: 13 December 2010 19:54
>> To: Gromacs Users' List
>> Subject: Re: [gmx-users] HBOND probability
>>
>> Poojari, Chetan wrote:
>>> Hello Justin,
>>>
>>> I commented out the lines from 151-161
>>>
>>> # unless ($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.
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------------------------
>>>>> ------------------------------------------------------------------------------------------------
>>>>> Forschungszentrum Juelich GmbH
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>>>>> 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 at gromacs.org
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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
>>
>> ========================================
>> --
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at 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 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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at 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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