From: Jeremiah Babcock (zhc605_at_my.utsa.edu)
Date: Fri May 30 2014 - 14:40:15 CDT

 Josh,
    Excellent!

Jeremiah B.

On Fri, May 30, 2014 at 7:11 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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>
> 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> 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
>>>
>>>
>>> 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/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>>
>>
>>
>>
>>