[gmx-users] HBOND probability

[Justin A. Lemkul]

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

========================================