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Re: [modeller_usage] Atom has GB/SA radius 0.0000.

Joaquim Rui Rodrigues wrote:
> I made some changes to the script examples/automodel/loop.py to do
> loop refinement with dope_loopmodel in the
> presence of ligands. While this used to work well with modeller 9v4,
> with 9v5 I am getting the following error:

Actually, it didn't work with Modeller 9v4. ;) 9v4 would happily run
with zero GB/SA radii, but this would result in infinite terms creeping
into the scoring function, which would give unpredictable results. So in
9v5 an explicit check is made for sane radii.

> The atom is an MG ion. From solv.lib: 
> #      RSOL   GBSA    ASP   ASPW   SCKS   OONS    JRF
> MG    0.000  0.117  0.000  0.000  0.000  0.000  0.000 ! Magnesium Ion
> I suppose I should change the value of RSOL. Is there any recomended
> value?

That is exactly right - RSOL is the value that needs to be changed. But
if we had a recommended value, it would be in there already. ;) I
suggest you check in the literature and perhaps in other MM packages
such as CHARMM.

> I foresee more problems for other atom types as solv.lib seems to
> have radii data only for protein atom types...

Yes, this is true, because that's all we've used GB/SA for ourselves.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage