Re: [modeller_usage] READ_MODEL error: MODEL atom not classified

[Modeller Caretaker <>]

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
-- 
             http://www.salilab.org/modeller/
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