From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Fri May 30 2014 - 18:33:20 CDT

Thank you all for such a great help ...

On Sat, May 31, 2014 at 4:40 AM, Jeremiah Babcock <zhc605_at_my.utsa.edu>
wrote:

> 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/
>>>>
>>>
>>>
>>>
>>>