[gmx-users] Hydrogen bonding

[Andrew Horsfield]

> Resolution != error. The error is much smaller, and could be assessed by
> looking at B factors.

I apologise for my ignorance! The average B factor for the non-hydrogen
atoms is 0.181nm^2. How do I convert this into an error?

> So how good was the agreement (RMS,H-bonding) straight after docking?

Using the best geometry from the docking:

   Docking   Gromacs   Experiment
   ------------------------------
     2.96      3.11      2.75
     2.61      3.02      2.88

So the relaxation had the effect of extending the hydrogen bonds.

Cheers,

Andrew