When I get the models from modeller, there are always some atom clash”£
How to solve this problem?
You can certainly try to refine these models using the force field of
your choice if you feel the clashes are too severe. Modeller includes
the CHARMM forcefield so should tend to avoid generating clashes in the
first place, but conflicts with other restraints (e.g. distance
restraints from your templates) may interfere with this.