From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Sep 16 2013 - 10:34:05 CDT

VMD's definition of a hydrogen bond isn't what you or I would use, since
VMD itself knows very little about chemistry. By default, it just looks
for atoms within a cutoff distance of one another and with a hydrogen
within 30 degrees of a straight line between them. Thus if your
atomselection contains carbons and aliphatic hydrogens, it may manage to
find some carbons that meet the distance and geometry criteria, and draw
the bond accordingly. If you want to exclude them, add something like "
and not name "C.*" " to your atomselection, which will exclude all
carbons, and thus probably get rid of the cyan ones.
-Josh

On 09/16/2013 10:24 AM, Research Jubilant wrote:
> Thanks for that explanation. But what is the reason that I see a bond
> between oxygen and a hydrogen attached to aliphatic carbons in default
> color when I am showing the HBonds in VMD?
> What does this ever have to do anything with HBonds?
>
> Thanks
> J
>
>
> On Sun, Sep 15, 2013 at 5:11 PM, Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
> Based on my own observations, colors are based on the name of the
> atom that "owns" the hydrogen in the topology. By default, oxygens
> are red, nitrogens are blue, and carbons are cyan (the lightish
> green). So a "hydrogen bond" from a water hydrogen to ammonia
> would be red, but a ammonia hydrogen that is shared with water
> would be a blue dashed line.
> -Josh
>
>
> On 09/13/2013 12:38 PM, Research Jubilant wrote:
>> Hello all VMD users,
>>
>> I'm using VMD's hydrogen bond capability from the Graphical
>> Representations tool. I get the Hbonds displayed in different
>> colors (mainly blue, red and light green, which is the VMD's
>> default color when any molecule is loaded) when I colored them by
>> default 'Name'. I checked the previous discussions about it in
>> the forum and also in userguide but no helpful information.
>>
>> Does anyone clarify the meaning of the colors shown in VMD for
>> Hbonds?
>>
>> Thanks
>>
>> J
>
>