[Chimera-users] Inquiry about hydrogen bond analysis- important

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 8 09:14:21 PST 2018

Dear Mohamed,
Different hydrogen bond calculations use different methods and parameters, so it is not surprising to get small differences unless you use exactly the same method and parameter values.   Some methods care about the angles, some only care about distances, sometimes it depends on the atom types, and the distance and angle cutoffs can vary.  The Chimera method is described here:

However, I don’t see any reason to prefer different results than in Chimera, because when I use Chimera to calculate ligand-receptor H-bonds on 1DB1 with the default parameters, I get the same H-bonds as shown in Fig 3D of the paper describing this structure:


Secondly, 1DB1 does not have hydrogens in it.   If you use Chimera to find H-bonds on a structure without hydrogens, it will imagine their possible positions when doing the calculation.  If you add hydrogens before doing the calculation, it may decrease the number of H-bonds found because then it only uses the hydrogen positions given, instead of imagining multiple possible positions.

Thirdly, PDB format does not contain bond orders, and I have no idea what Maestro may have done to change the file or why you think it is incorrect.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 7, 2018, at 5:33 AM, Mohamed S. Nafie <mohamed_nafie at science.suez.edu.eg> wrote:
> Chimera team.
> I made the hydrogen bond analysis for the co-crystallized ligand for 1DB1 receptor. it makes on the PDB 6 hydrogen bonds through both oxygen and hydrogen of the hydroxyl group (three of both) with the amino acids residues in the binding site, Also chimera forms 6 but through oxygen of hydroxyl group only. This my first question why? 
> The second question is the structure of the Co crystallized Ligand is not correct, when I adjust the bond order of it by Maestro and save it as pdb and reopen it by Chimera, it forms only two hydrogen binds why? 
> Please try to help me in this question, because I need it necessary
> Thanks
> Mohamed S. Nafie 
> Assistant lecturer Chemistry Department,  
> Faculty of Science,  Suez Canal University 
> Ismailia, P.O(41522), Egypt
> Mobile: +201065072524

More information about the Chimera-users mailing list