[gmx-users] Hydrogen bonding

[Daan van Aalten]

Andrew

Do you mean you removed the highly ordered crystallographically observed
water molecules in the active site? This is highly undesirable whether you
simulate in vacuo or in a solvated box. Quite a few of these water
molecules serve to establish key hydrogen bonding networks that are
essential for maintaining a proper fold. I have always thought this is one
of the main reasons why most people get high RMSD's from starting
structures. Once removed these water molecules are never replaced exactly
by the solvation algorithm.

cheers

Daan


On Wed, 30 Jan 2002, Andrew Horsfield wrote:

> Hi Daan,
> 
> > 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.
> 
> I used PRODRG to build the topology. I then tried two sets of charges: the
> ones from PRODRG, and charges from an electronic structure calculation
> (using DMol). It did not make a big difference which I used.
> 
>     PRODRG     DMol      Experiment
>     -------------------------------
>      2.88      3.17         2.75
>      3.41      3.25         2.88
> 
> Note that the Gromacs results here do *not* include the solvent. I have 
> not tried the PRODRG calculations with solvent. I will set this going now.
> 
> Cheers,
> 
> Andrew
> 


##############################################################################
 
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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