[gmx-users] HBOND probability

Justin A. Lemkul jalemkul at vt.edu
Mon Dec 13 19:54:38 CET 2010



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
> 
> ========================================
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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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