First, try using a file that has already been tested, such as this file generated from the GLYCAM Web-Builder OR PDB ID: 3SGJ.

If those files work properly, but your original does not, check the file to ensure the pdb is in the proper format (compared to the provided files). For example, a .pdbqt file generated by AutodockTools includes an additional column of charges that is unusual for PDB files. This file type creates the following error on the command line:

ERROR) can't use non-numeric floating-point value as operand of "+"

Removing the column of charges fixed the issue in this situation. If the problem persists, please contact us.