[gmx-users] perl script for g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Tue Nov 30 00:20:01 CET 2010


Did you inspect the contents of hbmap.xpm? There's a header followed by 
matrix data. You can think of the matrix as ones and zeroes, represented 
by the characters 'o' (= one) and ' ' (space = zero). As such, the rows 
of the matrix are vecors containg ones and zeroes. Two such vectors can 
easily be multiplied elementwise. If you write a program or script in 
your language of choice, that reads the matrix data as ones and zeroes 
instead of 'o's and ' 's, and then multiply the vectors elementwise, 
then that part of the job is done. I'd do it using python, but 
everything form matlab to C will do.

Is it clearer now?


leila karami skrev 2010-11-29 15.37:
> 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

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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