Subject: [modeller_usage] Atom has GB/SA radius 0.0000.
From: "Joaquim Rui Rodrigues" <>
Date: Tue, 2 Dec 2008 10:37:35 +0000
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...
Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)