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 <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>>
>>
>>
>> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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