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Re: [modeller_usage] changes in MODELLER9 optimization & DNA denaturation

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
--
             http://www.salilab.org/modeller/
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