[gmx-users] Occupancy warning

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 19 11:14:01 CET 2004

On Fri, 2004-03-19 at 10:49, Zhiguo Liu wrote:
> Dear gmx-users ,
>      When I did pdb2gmx to my homology protein models, I always received the warning
>   "  
>   WARNING: there were 620 atoms with zero occupancy and 0 atoms with
>          occupancy unequal to one (out of 2139 atoms). Check your pdb file.
>   "
> Do I always have to check my pdb file to get rid of this warning message? I don't want to optimize my structure too much, for this may change some essential features from the template protein. Or I can just leave it alone?
It is just a warning intended to point you to the original structure.
Sometimes crystallographers put in atoms with zero occupancy when they
know the atoms are there, but when they don't see them in the structure.

If you know why you have those occupancies set to zero, you can ignore
the message
> Best Regard!
>                                  Zhiguo Liu
>                                  DDDC
>                                  Chinese Academy of Science
>                                  Shanghai,China
>                                  zgliu at iris3.simm.ac.cn
>                                  2004-03-19
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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