[Chimera-users] FindHBond tool not finding H-bonds with sulfur?

[Gustavo Seabra]

Hi there,

I’m trying to use the findHBond tool to count Hbonds in a system. However, I noticed ti does not find any HB involving sulfur atoms in my system.

I’ve put together a simple example system here to show what I mean. After opening the files, I do:

1. Select the ligand (Select > Residue > LIG)
2. Tools > Surface/Binding Analysis > FindHBonds
3. Find These Bonds: Both
4. Relax H-bond constraints: (I tried even relaxing to 1A and 30deg, with no change)
5. Select “Only find H-bonds with at least one end selected”
6. Hit Apply.

Chimera does find some HBonds involving nitrogen and oxygen, but no HBond is found involving the sulfur atom on the ligand, even though there is a serine (Ser525) close enough to make a HBond to the ligand S atom.

So, I wonder what I am doing wrong here? Am I skipping any steps? I have checked in a different program (PoseView) and it can find the bond with no problem.

Thank you very much,

--
Gustavo Seabra
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