[Chimera-users] H Bonds in MD simulation

[Elaine Meng]

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
>