[Chimera-users] H Bonds in MD simulation

snoze pa snoze.pa at gmail.com
Thu Jan 28 14:36:25 PST 2010

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


On Thu, Jan 28, 2010 at 3:16 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi S,
> If you are recording a movie file, just do it for every step.  The playback
> will be slower but the resulting movie will not.  If you are just doing it
> for your own viewing, it is up to your own judgement how often it should be
> done.  Most accurate would be every step that is in your trajectory, but
> that will slow down the playback.
> As described in the manual,
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>
> findhbond uses several different distance and angle cutoffs depending on the
> donor and acceptor atom types.  Those cutoffs are based on very
> high-resolution small molecule structures, and we have found that for PDB
> structures in general (macromolecules and typically not as high resolution)
> the results are best with some relaxation of the strict values.  So for
> example if the strict cutoff is 1.0 A, with 0.4 tolerance, the resulting
> cutoff would be 1.4 A.
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jan 28, 2010, at 1:06 PM, snoze pa wrote:
>> Thanks Elaine for your prompt reply. Do you think if it is good to
>> calculate the hbonds after every 10ps snapshot from hbonds menu. I
>> want to count how many hbond are lost with time. When I am using this
>> trick then I can see no more broken hbonds. Also another question
>> related to Relax constraints, it is 0.4 A; what that mean? is it same
>> as donor acceptor atom distance?
>> thank you.
>> S

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