[gmx-users] distance and angle cutoff for hydrogen bond

[Justin A. Lemkul]

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.
> 
> 

-- 
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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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