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Re: [modeller_usage] question about mutate_model

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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage