RYAN PAVLOVICZ wrote: > Hi. I just upgraded from MODELLER8v2 to 9v1 and am experiencing > problems when modelling a protein-DNA complex in that the DNA is > denaturing after optimization. When I use the same modelling script > in 8v2, the DNA stays in its double-helical form, even when i use > md_level= refine.very_slow. > > Can anyone explain to me what changes in the optimizers were made > that cause this denaturation? I am using the MODELLER residue types > ADE, GUA, CYT, and THY for the modelling.
This behavior change is not due to modifications in the optimizers, but rather in the restraints imposed on HETATM residues. In short, inter-residue restraints on HETATM residues were calculated in Modeller 8v2, but not in 9v1. This can be corrected in 9v1 by applying the patch at http://salilab.org/modeller/wiki/Patches
Ben Webb, Modeller Caretaker