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.