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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