[gmx-users] occupancy

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jan 19 20:44:40 CET 2010

Hi Carla,

You can do lots of things. You can edit the occupancy field by hand,
or do it with a tool like sed. You can also neglect the warning,
provided that you're pretty sure the structure is okay. Partial
occupancies occur when atoms can not be exclusively assigned to a
single position. In those cases pdb2gmx takes the first location
listed. Occupancies of 0 occur when an atom position is completely
guessed or modeled in. Check the PDB file format to learn more.



On Tue, Jan 19, 2010 at 4:56 PM, Carla Jamous <carlajamous at gmail.com> wrote:
> Hi,
> I'm encountering a problem with pdb2gmx & occupancy. I searched the mailing
> list & followed this advice: "do NOT throw away crystallographic water
> molecules before you run genbox". I kept my pdb's water mlolecules & ran
> pdb2gmx.
> But still I get this warning:
> " there were 0 atoms with zero occupancy and 1 atoms with occupancy unequal
> to one (out of 2658 atoms). Check your pdb file."
> What can I do to stop having this warning?
> Thanks
> Carla
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist

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