I used MUTATE_MODEL to mutate ALA into ILE. now the ILE bumps into another residue. turning the dihedral of the ILE sidechain manually in a viewer will solve this. but I want to include an automatic minimization process in the mutate.top script, which will do it for me. In the FAQ section I saw the question 2. which describes a similar problem, it refers to examples/tutorial-model/model-segment.top . but it's not so clear to me how to merge the mutate.top and the model-segment.top in one both_steps.top, does it really need an alignment for doing this optimization of one residue?
thank you for good tips.