[gmx-users] perl script for g_hbond / summary_HBmap.dat

Erik Marklund erikm at xray.bmc.uu.se
Wed Nov 24 16:26:56 CET 2010


The -ins option is badly broken as far as I know. Don't expect it to 
work anytime soon.

The hbmap.xpm depicts the existence functions h for all hydrogen bonds 
as functuions of time. A red pixel means that the hydrogen bond is there 
(h=1), white means that the hbond is broken (h=0). If you multiply h(t) 
for a certain water molecule interacting with protein with h(t) for the 
same water molecule interacting with DNA, then theresulting existence 
function will be unity only at those frames where the water hbonds to 
both protein and DNA. If you do that for all waters and store the 
resulting existence functions in xpm-format you can run Justin's script 
on your new data. You need to create a corresponding index file too of 



leila karami skrev 2010-11-24 16.07:
> Dear Erik and Justin
> Thank you so much for ypur help.
> yes I mean water mediated hydrogen bonds (protein-H2O-dna).
> since I'm beginner in perl script, please clarify your answer and 
> explain more. what is your mean of
> existence functions exactly?
> do using of -ins option in g_hbond tool help me?
> -- 
> 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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