[gmx-users] HBOND probability

[Justin A. Lemkul]

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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-- 
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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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