If an error occurs in building the polypeptide chain, reading commands, or opening files during a batch mode run FANTOM will stop. If an error occurs in interactive mode the user must retype the command correctly, or correct the input data files before repeating the command. Error messages will be written to the overview file whenever an error occurs. The messages are usually self-explanatory and help the user to locate the error.

If the execution of a command consists of several independent calculations the program will not stop if an error occurs in one of them. Instead this calculation will be skipped by the program and a warning message written to the protocol. For example, if one of the distance constraints can not be read properly, it is skipped and a warning message is written to the protocol.

Warning messages are also written, if the beginning of a residue can not be fitted properly to the end of the preceding residue; if FANTOM has to adjust input data (for example replacing a 0 by a small positive number to avoid division by 0); or if commands don’t make sense with respect to preceding commands (for example if the command atoms is used after the conformational energy has been switched off by physical none).

Many error messages can be avoided by a simple check of the quality of an input PDB file (command inpdb), especially naming and numbering of atoms and residues.