[gmx-users] occupancy

[Daan van Aalten]

Hi Yuhua

To decide which complex to use, take the following into consideration:

1) look at the B-factor column in the PDB file. Guesstimate the average
   B-factor of the protein and compare that to the average B-factor of
   the ligand. If <B>protein is 20 and <B>ligand is 60 it means there
   will have been quite a bit of uncertainty in placing the ligand in the
   electron density.

2) look at the resolution of the diffraction experiment. Was one of the
   complexes refined to much higher resolution (e.g. 1.5 Angstrom) than
   the other (e.g. 2.9 Angstrom)?

3) the atoms that have zero occupancy - where are they? Buried deep in the
   active site, or completely solvent exposed? If the latter I would not
   worry too much about the atoms with 0 occupancy as they are not
   interacting significantly with the protein anyway.

Final word of advice - do NOT throw away crystallographic water molecules
before you run genbox (as I think most people on this list do!) and look
carefully at the geometry of the small molecule - are there strange bond
lengths/angles/impropers? If so, don;t use it as start for building a
topology.

cheers

Daan



On Thu, 19 Feb 2004, Yuhua Song wrote:

> Hi,
>
> I have a pdb file for small molecule, when I use pdb2gmx -f *.pdb, it shows
> "Warning: there are 4 atoms with zero occupancy and 10 atoms with occupancy
> unequal to one".
>
> After I search mailing list, the answer about the occupancy is "that means
> that the crystallographers have refined the structure with partial
> occupancy, i.e. they are not sure the atoms are there all the time. These
> atoms may also have high B-factors, and/or have multiple
> different conformations in the pdb file."
>
> My questions is if I ignore the warning, it will cause some troubles?
>
> Also, for the same molecule, but with different PDB file, with pdb2gmx, it
> shows that " All occupancy are one"
>
> So, based on the situation, which PDB file for the small molecule will be
> the best for the simulations?
>
> Thank you very much,
>
> Yuhua
>
>
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##############################################################################
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow / Reader
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: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk