VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Apr 29 2019 - 11:17:35 CDT

And the reason this works is that internally it *isn't* measuring the angle D-H-A, but is actually measuring the angle D-A-H (or A-D-H, I forget... in any event, the hydrogen is on one end of the interaction). This means that small angles mean that the three atoms are roughly co-linear.

-Josh

On 2019-04-27 08:38:32-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Hi,
     If the cut off is 45 degrees, it means less than or equals to 45 degrees.
With Regards

On Sat, 27 Apr 2019, 19:22 Saikat Pal, <saikatpaliitg_at_remove_yahoo.com<mailto:saikatpaliitg_at_remove_yahoo.com>> wrote:
Dear all,
I am very confused about the Hydrogen bond calculation using VMD h-bond plugin https://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/ . In hydrogen bond plugin If I select Angle cut off = 45 degrees then what should I write in angle cut off criteria <D-H-A is less than equals to 45 or greater than equals to 45?
Thanks and Regards,
Saikat Pal