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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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