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)