[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] Atom has GB/SA radius 0.0000.

Dear Modellers,

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:
e_gbsa__234E> Atom     8137 (type      112) has GB/SA radius        0.0000.
              Radii must all be greater than zero. Please edit
              the library file (e.g. modlib/solv.lib) to set
              a correct radius for this atom type.

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

Many thanks,
Rui Rodrigues

Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)