VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri May 30 2014 - 07:11:42 CDT

Hi guys,

Read the hbond plugin manual
(http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/). If you are using
the GUI, ask it to calculate info for unique h-bonds. Then it won't
aggregate hbonds by residue, and all the numbers will be less than 100%.

-Josh Vermaas

On 05/30/2014 04:25 AM, Jeremiah Babcock wrote:
> Bharat,
> I had the same question but never solved it. I put a lot of time
> thinking of scripts to write. It doesn't seem like you have. However,
> I second the question.
>
> --
> Jeremiah B
>
>
> On Thu, May 29, 2014 at 9:23 PM, bharat gupta
> <bharat.85.monu_at_gmail.com <mailto:bharat.85.monu_at_gmail.com>> wrote:
>
> Okay.. if thats the case, then how can I get the hydrogen bond
> information for each interacting atom of a residue .??
>
>
> On Fri, May 30, 2014 at 11:18 AM, John Stone <johns_at_ks.uiuc.edu
> <mailto:johns_at_ks.uiuc.edu>> wrote:
>
> Hi,
> JC Gumbart already answered your question previously, did
> you see
> his response?:
> >
> > This can happen because two residues can form more than one
> h-bond at once.
> >
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu <mailto:vmd_at_ks.uiuc.edu>
>
>
> On Fri, May 30, 2014 at 10:55:55AM +0900, bharat gupta wrote:
> > Hi,
> > I calculated the hydrogen bond occupancy for a residue
> during 10 ns
> > simulation. I found that for one hydrogen bond pair the
> occupancy is
> > around 130%?? Why the percentage is more than 100%??A
> > --
> > Bharat
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> Phone:
> 217-244-3349 <tel:217-244-3349>
> http://www.ks.uiuc.edu/Research/vmd/
>
>
>
>