[Chimera-users] H Bonds in MD simulation

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 28 14:59:04 PST 2010

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  

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

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