atila petrosian wrote:
Dear gromacs users
in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor
- Donor - Hydrogen)
-r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)]
I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A.
and angle of 30 = acceptor-donor–hydrogen angle.
is my think true?
That's what the manual says.
if I want following criterion for hydrogen bond analysis, is [ -r 3.5
and -a 135 ] true?
No. Gromacs uses nm for distances. With -r 3.5, you calculate H-bonds that are
3.5 nm away. An angle of 135 for A-D-H means the H atom is pointed away from
the acceptor, indicating that there really isn't a hydrogen bond.
-Justin
donor-acceptor distance (d_DA ) ≤ 3.5 Å and the donor–hydrogen-acceptor
angle (α_DHA ) ≥ 135°.
any help will highly appreciated.
--
========================================
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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