[Chimera-users] H Bonds in MD simulation
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.
> 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
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