On 4/21/10 10:20 AM, Thomas Evangelidis wrote: > I want to build models of a protein with ATP with the dopehr_loopmodel > method. The problem is when I include ATP in the alignmnet I get the > following error:
In order to calculate the GB/SA interaction between the loop and the ligand, Modeller needs to know the radii of all atoms in the ligand. You'll need to modify solv.lib as suggested to add radii for each atom type in ATP. I can't tell you what values to use, since they have not been parameterized, but you could simply copy those for similar-looking atom types. Alternatively, use the regular loopmodel class, which does not include GB/SA.
There will be an automatic workaround for this issue in the upcoming 9v8 release; ligand atoms will simply be treated as having a very small (but non-zero) radius for GB/SA.
Ben Webb, Modeller Caretaker