[gmx-users] perl script for g_hbond

[Justin A. Lemkul]

Olga Ivchenko wrote:
> Dear Justin,
> 
> I ran you H bond frequency script and I got the following result. I am 
> understanding that the occupancy of H bonds is on the writeside, but 
> somehow in donor and acceptor column there is the residue name not atom 
> type. I am not quiet good iunderstanding my output. Please can you 
> advice me on this?
> 

Something is very wrong with your input.  Probably your index file is incorrect. 
  Have you read the requirements in the header of the script?  You can't pass a 
standard hbond.ndx (output of g_hbond -hbn) to the script.  It requires that the 
.ndx file supplied contain only the [hbonds_...] section.

-Justin

> #    Donor                    Acceptor                 % Exist.
>                                                                     0.040
>       LIG1            C1          LIG1            C2         0.680
>       LIG1            H7          LIG1            H9         0.040
>                                                                         
> 0.040
>       LIG1            N3                                            0.360
>       LIG1            N2                                            0.120
>       LIG1            O2                                           0.040
>                                                                        0.120
>       LIG1            N1          LIG1            O2         0.120
>                                                                         
> 0.040
>                                                                         
> 0.160
>                                                                          
>   0.040
>                                                                         
>     0.040
>                                                                        
>    0.040
>                                                                        
>    0.040
>                                                                          
>     0.080
>                                                                         
>      0.200
>                                                         
>                    0.040
>                                                                         
>    0.040
>                                                                          
> 0.200
>                                                                         
> 0.080
> 
> 
> best,
> Olga
> 
> 2010/11/29 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     Olga Ivchenko wrote:
> 
>         Hi Leila,
> 
>         I am also have a task to calculate H-bonds frequency through the
>         over all trajectory in gromacs. Please can you send me Justin's
>         script. If he does not mind.
> 
> 
>     I have several analysis scripts available to the public on my website:
> 
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
> 
>     -Justin
> 
>         Yours sincerely,
>         Olga
> 
>         2010/11/29 leila karami <karami.leila1 at gmail.com
>         <mailto:karami.leila1 at gmail.com> <mailto:karami.leila1 at gmail.com
>         <mailto:karami.leila1 at gmail.com>>>
> 
> 
>            Dear Mark and gromacs users
> 
>            thanks for your time and consideration.
> 
> 
> 
>            you said by multiplying the existence functions for hbonds
>         between protein and water and the hbonds between water     and
>         DNA, then using Justin's script, I can obtain percentage each
>         water medited hydrogen bond during trajectory.
> 
>            and also you said I need to create a corresponding index file
>         too.
> 
>            I don't know where should I start for multiply two existence
>         functions?
> 
>            please explain about it more.
> 
>            any help will highly appreciated.
> 
> 
> 
>            
> 
> 
> 
> 
>            --
>            Leila Karami
>            Ph.D. student of Physical Chemistry
>            K.N. Toosi University of Technology
>            Theoretical Physical Chemistry Group
> 
> 
> 
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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 <http://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

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