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

Erik Marklund erikm at xray.bmc.uu.se
Wed Nov 24 15:48:42 CET 2010


If you mean interactions bridged by a watermolecule, Protein-H2O-DNA, 
then I don't know of any gromacs related tools for this. You need to 
write your own tool for this. One way would be to multiply the existence 
functions for hbonds between protein and water and the hbonds between 
water and DNA, then use Justin's script to get the percentage.


leila karami skrev 2010-11-24 15.42:
> Dear Justin
> thanks for your attention
> with chang of hbond.ndx file my problem was solved.
> I have another question about g_hbond: if I want to obtain same 
> information (percentage of existence of each hbond during my 
> trajectory) about water mediated hydrogen bonds between protein and 
> dna, for obtaining of hbond.ndx and hbmap.xpm files from g_hbond tool, 
> what groups should be select?
> in previous state (protein-dna direct hydrogen bond), I selected 1) 
> protein and 2) dna.
> -- 
> 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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