Marzinek, Jan wrote:
Hi,
I have a question related to the calculation of hydrogen bonds in
Gromacs. As I read in Manual it comes from the distance between donor
and acceptor ( <= 0.35 nm) and the angle <=30 degr beween hydrogen and
acceptor. The question is - why 30 degr? How is it related to the reality?
Hydrogen bond strength decreases with distance between the donor and acceptor
and with deviation from linearity. A survey of crystallographic structures
shows that these are generally accepted criteria. There is literature on this
that dates back many decades.
The second thing is the claculation of the accessible surface area
(g_sas) of the molecule for instance? It is not explained in manual and
I am really curious how g_sas makes these calculations.
I'd suggest you look at the citation provided in the "PLEASE READ AND CITE THE
FOLLOWING REFERENCE" section printed when running g_sas :)
-Justin
As my supervisors do not know the gromacs their questions are always
about such details :)
However, I think it is really important to understand what you are
really doing using commands in Gromacs which provide you with really
detailed results.
Thank you in advance,
Jan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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