VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Jun 04 2014 - 22:09:45 CDT

What are your selections exactly? From the manual: "The plugin provides
options for up to two selections *(which should not overlap)*" (emphasis
is mine). If you did residue 14 as selection 1 and "protein" as
selection 2, strange things may happen. This does seem strange, but the
code behind this isn't exactly new, so odds are its just a problem with
the inputs you are feeding it. Are there perhaps 2 OD1 atoms somehow in
residue 41?

-Josh Vermaas

On 06/04/2014 07:37 PM, bharat gupta wrote:
> 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 <mailto: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 <mailto: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 <mailto: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
>> <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/
>>
>>
>>
>>
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