To run MODELLER with the script file model-default.top, execute the following command:
mod model-default
A number of intermediary files are created as the program proceeds. After about 30 seconds on a Pentium III workstation, the final 1fdx model is written to file 1fdx.B99990001. Examine the model-default.log file for information about the run. In particular, one should always check the output of the CHECK_ALIGNMENT command, which you can find by searching for `chkaln'. Also, check for warning and error messages by searching for `_W>' and `_E>', respectively. There should be no error messages; most often, there are some warning messages that can usually be ignored.