On Tue, Apr 27, 2004 at 11:52:16AM +0200, Sascha Tayefeh wrote: > I am trying to get warm with modeller-usage by checking out the > official manual's examples. > > For some reason, the READ_MODEL command does not work. Here's my > input/output: > > > *************** INPUT ************************** > READ_TOPOLOGY FILE = '/soft/modeller6v2/modlib/top.lib', TOPOLOGY_MODEL = 3 > READ_PARAMETERS FILE = '/soft/modeller6v2/modlib/par.lib' > READ_MODEL FILE = '1P7B' > > *************** OUTPUT ************************** > iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL > iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL > > > Using different pdbs (eg. manual's suggested 1fas), I get the same error > with different residues. > > *************** OUTPUT ************************** > iatmcls_286W> MODEL atom not classified: TYR:OT1 TYR > iatmcls_286W> MODEL atom not classified: TYR:OT2 TYR
These are warnings (W>) not errors (E>). READ_MODEL does work.
> I have checked the pdbs for OT1 - there is simply no such entry, so: > what's the problem? Also, I have tried modeller on different platforms > (linux, irix etc).
The OT1 atom is added by the C terminus patch residue, as given in top.lib. The warnings you're seeing should be for the last residue in your PDB each time, which has this patch.
This warning means that the two added carboxylate oxygens (OT1 and OT2) do not have defined atom classes for statistical potentials; these atom classes are usually given in modlib/atmcls-melo.lib. The warning can be ignored unless you are using these classes (usually this is only the case in loop modeling) and the effect of the statistical potential on the terminal oxygens is significant. You can also fix it (as it has been in the next version of Modeler) by changing the line which reads ATOM TYR OXT in modlib/atmcls-melo.lib to read ATOM TYR OT1 ATOM TYR OT2 and so on.
Ben Webb, Modeller Caretaker