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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