[gmx-users] Hydrogen bonding

[Daan van Aalten]

Hi Andrew

Resolution != error is not an entirely correct statement. Yes, the
B-factor is an indication of disorder, but on top of that in a 4 Angstrom
structure there can easily be an uncertainly of a few ten's of Angstroms
in the coordinates, regardless of how high or low your B-factors are.
Also what matters is the *relative* B-factor, as B-factors themselves are
only a fudge number to model the SUM of "static" and "dynamic" disorder in
the structure. And then we're not even talking about the fact that
B-factors in a packed crystal do not necessarily have to agree very well
with positional mean square fluctuation calculated from an MD trajectory.

So, apart from just looking at your ligand, you might also want to look at
what EM did with the protein structure itself, can you see shifts of
0.1-0.2 Angstroms there? (most likely). This is caused by a combination of
sub-optimal geometry in the crystal structure, solvation effects and small
forcefield artefacts.

Also, how did you generate you *ligand* topology. If PRODRG, did you check
that all the non-C atoms actually carry a small partial charge? Not all
chargegroups are recognized yet and I would certainly check these before
using the topology.

cheers

Daan

On Wed, 30 Jan 2002, Andrew Horsfield wrote:

> > 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
> 
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

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