Hi, Robin.
I think it could be extracted using the -hbm and -hbn output (pretty
much everything can). Write a python script that reads the files and
checks which donors don't participate in hbonds at each frame.
Alternatively, if you want to hack gmx_hbond.c, i suggest the following:
Use the t_donors struct in (hb->d in gmx_hbond()) to create an bolean
array with one element per donor (or donor+H depending on what you want
to know in the end). Then set each element to TRUE whenever that donor
is acting as a hydrogen bond donor. At the end of each frame just go
through the array and write the number of non-donors to file. Clear the
array and attack next frame.
Erik
Robin C. Underwood skrev 2010-11-08 22.10:
Thanks for the prompt reply Justin, but I'm still not convinced that I can
extract the information I seek from the g_hbond program without modification.
I realize this wasn't clear in my initial message: I would like to know how many
OH donors are not participating in ANY hydrogen bonds.
If I calculate the number of non-hydrogen bound OH donors as the difference
between the number of pairs that meet the distance requirement, and the actual
number of hydrogen bonds (column 3 minus column 2 in hbnum), then I would be
over-counting, as this does not exclude pairs with OH donors that are also
included in a hydrogen bond with another O acceptor.
Robin
Quoting "Robin C. Underwood"<rcund...@purdue.edu>:
I would like to modify the g_hbond code (or preferably, know how to
implement
g_hbond if it is already capable) to count the number of non-hydrogen bound
water OH donors in a simulation. I define a non-hydrogen bound donor as one
that
does not meet the distance requirement, or one that may meet the distance
requirement for a hydrogen bond, but does not meet the angle requirement.
An inferred value of non-hydrogen bound OH donors is not exact because there
is
not a rigorously defined maximum value for the number of hydrogen bonds per
water, (e.g. a single OH donor may qualify as part of a hydrogen bond at two
adjacent water's O-acceptor sites, making the maximum possible number of
hydrogen bonds for the water of this particular OH donor greater than 4).
Is there a way to implement g_hbond to do this? If not, any specific
information
on what to consider, and how to modify the g_hbond source code to count
non-hydrogen bound water OH donors is greatly appreciated.
Robin
--
Robin C. Underwood
Chemistry Department
560 Oval Drive
West Lafayette, IN 47907
--
-----------------------------------------------
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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