[gmx-users] Hydrogen bonding

[Daan van Aalten]

Hi Andrew

I would say that's a pretty good agreement. You don;t mention a few
things, however:
- what is the RESOLUTION of the complex structure you are structure with?
  Uncertainty of coordinates in X-ray structures can easily be up to 0.2
  Anstroms!
- were the given values after EM or after MD?
- how did you generate your topology?

cheers

Daan

On Wed, 30 Jan 2002, Andrew Horsfield wrote:

> Hi,
> 
> I am looking at the interaction of a small molecule with a protein. The
> problem that concerns me is that interactions with other atoms in the
> protein are pulling the small molecule away from the site suggested by
> experiment, and I am trying to track down the root of this.
> 
> I suspect that hydrogen bonds are the key here. Gromacs gives only
> moderate agreement with experiment for the length of the hydrogen bonds I
> am interested in (distances are in Angstroms):
> 
>     Gromacs       Experiment
>     ------------------------
>       3.11          2.75
>       3.02          2.88
> 
> Is this what you would expect from a force field, or is it possible to get
> better agreement?
> 
> 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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