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 <jalem...@vt.edu <mailto:jalem...@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.lei...@gmail.com
        <mailto:karami.lei...@gmail.com> <mailto:karami.lei...@gmail.com
        <mailto:karami.lei...@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

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