On 2010-11-08 22.10, Robin C. Underwood wrote:
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.
check out the -nhbdist flag.
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
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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