VMD-L Mailing List

From: Anthony Ma (akma327_at_stanford.edu)
Date: Tue Apr 26 2016 - 17:57:06 CDT

Hello,

I'm emailing about a question regarding using the HBonds drawing method as
a way to extract hydrogen bonds information for a trajectory. I have been
able to use tcl commands to get the donor, acceptor pairs but there seems
to be duplicates for the same frame. With the setting of 3.8 distance and
70 Angle cutoff there are two lines being drawn between (index 75594 or
index 29778) query. I'm not sure how it's possible for two hydrogen bonds
to form between just a single pair of atoms, but any help regarding this
issue would be highly appreciated. Thanks!

On Tue, Apr 26, 2016 at 12:55 PM, Anthony Ma <akma327_at_stanford.edu> wrote:

> Hello,
>
> I'm emailing about a question regarding using the HBonds drawing method as
> a way to extract hydrogen bonds information for a trajectory. I have been
> able to use tcl commands to get the donor, acceptor pairs but there seems
> to be duplicates for the same frame. With the setting of 3.8 distance and
> 70 Angle cutoff there are two lines being drawn between (index 75594 or
> index 29778) query. I'm not sure how it's possible for two hydrogen bonds
> to form between just a single pair of atoms, but any help regarding this
> issue would be highly appreciated. Thanks!
>
> anthony
>