On 12/02/2013 11:01 AM, gbanoczi@mail.bme.hu wrote:
I have a problem with all hydrogen models, namely some of the amino acid residues chirality inverts in the final models.
Generally we recommend building heavy-atom-only models, as it is trivial to add hydrogens to the final models. It's entirely possible that hydrogens could pass "through" heavy atoms in the early parts of CG optimization (where VDW interactions are not considered) and then be trapped there - I suspect that's what's happening in your case. You could certainly try playing with the optimization schedule if you really want to build all-atom models.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage