From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Wed Jun 04 2014 - 18:37:26 CDT

Hi,

I checked again for hydrogen bonds of residue 14 with protein and this time
I used "Unique hbonds". Here's the output :

Found 2 hbonds.
donor acceptor occupancy
PHE14-Main-N ASP41-Side-OD1 140.99%
PHE14-Main-N ASP41-Side-OD2 5.41%

Now as you can see the % for the first hbond pair is 140%. How can this be
possible ??

On Sat, May 31, 2014 at 8:33 AM, bharat gupta <bharat.85.monu_at_gmail.com>
wrote:

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