[Chimera-users] H Bonds in MD simulation

snoze pa snoze.pa at gmail.com
Fri Jan 29 10:02:24 PST 2010

I checked the results with molmol and it seems chimera results are
correct. I want to save the number of hbonds in each frame. When I use
the command hbond in chimera script movie menu command then it prints
correct number of hbonds in every frame. Can you help me how to save
the results from each frame(total no of hbonds).
thank you

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

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