Ben: is it possible to save all warnings/errors in a .err file, so that
users can decide if they are something to worry about or not?
You can send the log output anywhere you want by using SetLogTarget. But
as Daniel points out, we had to choose between flooding the logs with
output when reading a PDB versus only warning once per atom type, and we
chose the latter.
That said, the log message is unambiguous:
WARNING Radius not found for type, default value is used "NP1"
Radii are looked up based on their CHARMM atom types, which are defined
in top_heav.lib (in the data/atom/ directory). By looking in
top_heav.lib, you can see that NP1 is a heme nitrogen. But there are no
van der Waals parameters defined for NP1 in par.lib in the NONB section,
so IMP will use a default radius. Unless you're planning to do detailed
electrostatic calculations involving heme groups (I wouldn't recommend
IMP for this anyway) this is nothing to worry about.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle