[gmx-users] occupancy

Ghermes Chilov Ghermes at belozersky.msu.ru
Fri Feb 20 09:37:01 CET 2004

Hello Yuhua,

YS> I have a pdb file for small molecule, when I use pdb2gmx -f *.pdb, it shows
YS> "Warning: there are 4 atoms with zero occupancy and 10 atoms with occupancy
YS> unequal to one".

I use to encounter this situation regularly, and my experience tells

1. You can close your yies on zero occupances: it really use to happen
with charged and mobile residues on the protein interface

2. It's better to check residues with partial occupances manually:
some conformers usually look more realistic than others (with respect
to H-bonding and etc) and some times models can even overlap one with
another (this is especially true for high-resolution structures, where
nearly all residues have several models)

alternatively you may use internet service to parse your structure:
say, WHAT IF http://www.cmbi.kun.nl/gv/servers/WIWWWI/
which does just the same (I hope)



More information about the gromacs.org_gmx-users mailing list