[Chimera-users] H Bonds in MD simulation
snoze.pa at gmail.com
Thu Jan 28 15:04:57 PST 2010
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
> 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
More information about the Chimera-users