leila karami skrev:
Hi
I want to obtain following parameters about water molecule and
hydrogen bonds in pr-dna simulation:
1) residence time of number of water mediated hydrogen bonds
2) life time of number of water mediated hydrogen bonds
3) number of water mediated hydrogen bonds
4) number of direct hydrogen bonds
Do g_hbond command is suitable for all of case mentioned above?
Any help will highly appreciated!
Yes and no. Only 4 in your list above is available directly. IF you're
willing to do some sort of programming in pretty much any preferred
language, you can extract 1-3 from the existence matrix of all hydrogen
bonds and its complementary index file (options -hbm and -hbn).
Lifetimes probably requires a bit more work, as the autocorrelation of
the existence function is needed, but there are plenty of tools for
that, e.g. xmgraxe or perhaps g_analyse.
--
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
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
[email protected] http://xray.bmc.uu.se/molbiophys
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