Re: [modeller_usage] conjugate gradients or molecular dynamics optimizations with automodel.make()

On 7/14/14, 8:39 PM, Li SUN wrote: > I have a question regarding the usage of automodel.make() for modelling > a protein structure from known structures. Does this function include > optimization methods e.g. conjugate gradients or molecular dynamics so > that it will output a structure close to the native state (lowest-energy > state)

Yes, of course. See http://salilab.org/modeller/9.13/manual/node485.html

Ben Webb, Modeller Caretaker