TABLE 5.

Troubleshooting table.

Step	Problem	Possible reason	Possible Solution
4	I uploaded a structure from my computer, but as soon as I submitted the job failed with the message: “Processing failed on receptor.” What is wrong?	Inconsistency with the PDB format. Note that homology modeling tools frequently fail to produce correct PDB format, e.g., by not placing a chain identifier.	Make sure that your file is in PDB format and has the required spacing between columns. Documentation with respect to the PDB file format can be found at: http://www.wwpdb.org/docs.html. Also, make sure that all ATOM records the PDB file contain only standard amino or nucleic acids.
	I entered a HETATM record to include in the calculation, but it was not recognized. What do I do?	At this point there is no option for considering heteroatoms (HETATM entries).	Remove the HETATM records.
6	I uploaded a structure from my computer, but as soon as I submitted the job failed with the message: “Processing failed on ligand.” What is wrong?	Inconsistency with the PDB format. Note that homology modeling tools frequently fail to produce correct PDB format, e.g., by not placing a chain identifier.	See TROUBLESHOOTING for Step 4.
10	My job keeps crashing even though my input file looks fine.	FFT grids are too large. This is typically caused by uploading a file output by homology modeling that has extremely large regions without a template, resulting in a tail that basically floats off into space.	Use the Structure Modification Option to remove the questionable parts of the model.
14	I cannot load the docking results into my molecular viewer.	Your viewer likely does not support multiple structures in one PDB file.	Try using PyMol, available at www.pymol.org