Anna Marabotti wrote: > I would like to use the script mutate_model to evaluate different > conformations of the same mutant side chain inserted in a protein. > Therefore I used the script "mutate model" as suggested in the Wiki > section, and repeated the procedure 5 times, expecting to obtain 5 > different conformations of the mutant side chain. Instead, I obtained > 5 identical proteins with side chains perfectly superimposable > between each others. How can I manage myself in order to obtain 5 > different models of the same mutation? Moreover, this is probably a > naive question, but since repeated MD cycles generally do not produce > identical results, why this protocol did not work in such a way?

If you start from the same initial conditions each time, your repeated MD cycles had better produce identical results, otherwise your science is not reproducable! Like most simulation packages, Modeller uses a pseudorandom number generator, so will yield reproducable results if the random seed is the same.

In your case, if you want to generate 5 different results from the mutate_model script, modify it to use a different random seed for each run. You can do this by changing the value of rand_seed when you create the initial environ() object.

Ben Webb, Modeller Caretaker