Lucas Bleicher wrote:
Let's call F(x) the Modeller objective function, which is minimized during the simulated annealing procedure. I'd like to use an alternative function to be minimized, say: F'(x) = F(x) + k.G(x) where F(x) is the original function, k is an arbitrary constant and G(x) is another function which can be calculated by an external program, given an intermediate model PDB file. Is there a way to accomplish this without having to edit Modeller's code? If so, how could I write a script to do this?
Unfortunately there is no way to do this with Modeller 8v1. We have, however, implemented such a feature in our development version of Modeller, and it'll be one of the features of the next public release.
Note that in order for such a function to be useful during optimization, your external program must also return the first derivatives of G with respect to the Cartesian coordinates.
Ben Webb, Modeller Caretaker
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