[gmx-users] occupancy

Yuhua Song yhsong at ccb.wustl.edu
Fri Feb 20 00:51:01 CET 2004


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,


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