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Article ID: 1174 - Last Modified: May 1, 2012

When I run a Glide, QSite, Impact, or Liaison job with a large protein, I sometimes get an error that there are "too many atoms". What can I do?

This error means that the number of atoms in the structure exceeds the internal limit that can be handled by the program. The limit since Suite 2010 is 90000 atoms. If your structure is too large, you will see error messages like:

rdmmct: Too many atoms (...) in current structure.
%IMPACT-W (warning): At line N
%IMPACT-W: Build Primary: Too many atoms for structure in: filename

%IMPACT-E (die): At line N
%IMPACT-E: CREATE: struc has too many atoms for executable.

If you encounter this error, you should consider trimming the size of your protein to fit the limit.

If you are using the impact command from a release prior to Suite 2010 or if you are not using a Maestro file for input, you must request an impact executable size that is large enough for your system, with -s huge for 40000 atoms, and -s extrahuge for 90000 atoms. The larger executables are not needed for Ligand Docking jobs, even if the receptor has more than 8000 atoms. All the required receptor information is encoded in the grid files, so the receptor structure itself never needs to be read during the docking job. Ligand structures are always much smaller than 8000 atoms, so the "normal" executable is sufficient for docking jobs.

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