rob yang wrote:
Hi list,
What's the geometric relation b/w the commonly used Donor-H-Acceptor
angle and the gromacs implementation of Acceptor-Donor-H angle? I guess
I don't quite follow why it's valid to define the ADH cutoff as 30
degrees, the same angle most commonly used to define DHA, which suggests
ADH==DHA?! Even the van der Spoel, J. Phys. Chem. B, 2006, 110 (9), pp
4393–4398 paper used the DHA<=30 degrees definition. I must be missing
something, and after hours of drawing triangles any help would be welcome.
This is kind of embarassing indeed, the confusion has lingered in my
head too long apparently. Obviously the DHA angle in a linear Hbond is
180, so it should either be 180-DHA or ADH. The ADH angle is what's
implemented in gromacs > 3.2.1, however in 3.1.4 it still was DHA. The
default maximum angle has changed from 60 in gmx 3.1.4 (based on Kabsch
and Sander 1983) to 30 (from 3.2.1 onwards, based on other literature).
So my paper uses ADH, even though it says DHA.
Thank you.
-Rob
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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