On 11/27/2009 06:11 AM, leuven wrote:
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.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage