[Chimera-users] H Bonds in MD simulation

Eric Pettersen pett at cgl.ucsf.edu
Thu Jan 28 15:00:32 PST 2010

I'd say you'd probably want to dump a list of the H bonds to a file in  
both programs (easy in Chimera at least) and find the differences and  
then look at the structure where the differences occur and assess for  
yourself which program is doing a more accurate assessment of the  
hydrogen bonding.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Jan 28, 2010, at 2:53 PM, Elaine Meng wrote:

> Different programs use different methods and cutoffs.  You could try  
> setting the tolerances to 0.0 if you feel the default Chimera method  
> is too permissive, but there is no reason to expect exactly the same  
> number of H-bonds from two different programs.  You would need to  
> look at VMD documentation to see how theirs are calculated, and at  
> Chimera's (link already sent in previous message) to know how they  
> are calculated, then decide which one you want.
> In Chimera, the angle and distance cutoffs depend on the atom types,  
> and the criteria depend on published data (the small molecule  
> structures).  In many other programs, the same cutoffs are used no  
> matter which atom types are involved.  I don't know how it is done  
> in VMD, however.
> I know of one paper where the authors tried both MolProbity (a  
> fancier method) and Chimera and said they usually gave the identical  
> H-bonds:
> Differences in the risk of celiac disease associated with HLA-DQ2.5  
> or HLA-DQ2.2 are related to sustained gluten antigen presentation.
> Fallang LE, Bergseng E, Hotta K, Berg-Larsen A, Kim CY, Sollid LM.
> Nat Immunol. 2009 Oct;10(10):1096-101
> 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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