[gmx-users] perl script for g_hbond

[Olga Ivchenko]

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?

#    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>

>
>
> 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>>
>>
>>
>>    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
>>
>>
>>
>>    --
>>    gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>
>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at
>>    http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>    Please don't post (un)subscribe requests to the list. Use the
>>    www interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>
>>    Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101213/cc682113/attachment.html>