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 5different models of the same mutation? Moreover, this is probably a naive question, but since repeated MD cycles generally do not produceidentical 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
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage