changes in MODELLER9 optimization & DNA denaturation
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.
Thanks!
ryan
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.
No changes in the optimizers were made between 8v2 and 9v1 (only the way in which they are called is different). So that's probably not what's causing your problem. It may be caused by some difference in your input files (maybe you weren't selecting the DNA for optimization in 8v2). I would need to see those input files to figure out what your problem was.
Ben Webb, Modeller Caretaker
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
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Modeller Caretaker -
RYAN PAVLOVICZ