As mentioned in the title, is there any way to ignore/skip loop modeling
in MODELLER9v21?
To be clear, you're referring to Modeller's handling of insertions, i.e.
regions of the model that don't align with a template, during
comparative modeling. (Loop refinement is a separate protocol that uses
a statistical potential rather than information from the alignment.)
Modeller builds a model for the sequence you give it. If you don't want
to build a model for a given sequence range, remove that range from the
alignment. If there's sequence on both sides of the removed region, you
might want to put a chain break there ('/' residue type) to prevent
Modeller from trying to make a peptide bond.