[Chimera-users] H Bonds in MD simulation

[snoze pa]

Thanks a lot Elaine! I highly appreciate your help and time.

On Thu, Jan 28, 2010 at 4:59 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> I forgot to mention: from looking at the images, I would say the Chimera
> results are more reasonable, because that's how beta-sheets form, with
> strand-strand hydrogen bonds.  In the VMD view, some strands lack H-bonds to
> the next strand in the sheet, or only have one.
>
> Of course, these statements are only qualitative, but it was my first
> impression.
> Elaine
>
> On Jan 28, 2010, at 2:36 PM, snoze pa wrote:
>
>> Hi Elaine, Thanks for your help. But somehow I am getting different
>> number of bonds in vmd and chimera. A snap shot of the  figure is
>> shown below.
>>
>> http://img191.imageshack.us/img191/9084/screenshotva.png
>>
>>
>> In VMD the Hbonds are calculated by show Hbonds and protein. Vms shows
>> 24 hbonds while chimera shows 38 hbonds. I don't know how to justify
>> this. I will highly appreciate your help. A snapshot is shown in the
>> link
>> http://img191.imageshack.us/img191/9084/screenshotva.png
>>
>> Thanks
>> s
>>
>
>