VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Oct 29 2013 - 09:57:38 CDT

Hi Himanshu,

It depends on what cutoffs you set. VMD measures hydrogen bonds by
considering the distance between the heavy atoms involved and the
position of the hydrogen bond between then. It may be that one bond is
just a little too long/not aligned in your trajectory, and you only see
2 instead of the expected 3. Relaxing the tolerances slightly may show
the third bond.
-Josh Vermaas

On 10/29/2013 02:16 AM, Himanshu Joshi wrote:
> Hi friends,
>
> I want to do some H bonds analysis for my AMBER DNA simulation.
> I have a confusion about its terminology, as it shows only two H bonds
> between guanine and cytosine in the detail log file which should be three,
>
> Why is it so ? Is it conventional or my structure has missing hydrogen
> bond at all which seems very less probable.
> Kindly give your valuable feedback.
>
> --
> */With Regards,
> HIMANSHU JOSHI
> Graduate Scholar, Center for Condense Matter Theory
> Department of Physics IISc.,Bangalore India 5600//12/*