I am running Modeller to build 500 homology models for a
methyltransferase. Now I am running serial job. Do you think I can run
parallel job? Or do you think I can submit the same script for 500 times
and I can get the same results with serial job?
Sure, you can do it either way. If you run as a serial job though, make
sure you specify a different random seed for each run, otherwise you'll
get the same model each time.