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

Erik Marklund erikm at xray.bmc.uu.se
Thu Nov 25 11:43:12 CET 2010

leila karami skrev 2010-11-25 11.37:
> Dear Erik
> 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.
> now I write steps. please check accuracy of them.
> 1) obtaining hbond.ndx and hbmap.xpm from g_hbond tool for hbonds 
> between protein and water.
> 2) obtaining hbond.ndx and hbmap.xpm from g_hbond tool for hbonds 
> between dna and water.
> 3) multiplying the existence functions
> how to multiply these two existence functions?
That's where your programming skills enter the picture.
> how to make new index file? should I write those lines from two 
> hbond.ndx file above in which particular water hbonds to both protein 
> and DNA?
Well, yes, if your new hbmap.xpm only contains those hbonds. In 
principle you coluld keep the empty existence functions too, but I see 
little point in doing so. The order in the index file must of course 
match that of your new hbmap.xpm.
> -- 
> 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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