[Chimera-users] H Bonds in MD simulation

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 28 13:16:58 PST 2010

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,
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 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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