dear Modellers,
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.
marc