Re: [modeller_usage] CHARMM atom type is out of range

[Modeller Caretaker <>]

zzj wrote:
> Hi, the problem was solved by deleting "inifile  = 'mgl.pdb'" in my 
> script. mgl.pdb is my template pdb file, without any further change. If 
> you still think this is not normal, I'll send the input files towrrow 
> when I get to lab.

If you specify an "inifile" it needs to be a set of coordinates of your 
model (usually from a previous optimization), not a template. If you 
leave out "inifile", then Modeller will automatically build an initial 
model (with a .ini file extension) based on your template(s) and the 
alignment. This is usually what you want, although sometimes the .ini 
file has such a bad structure (e.g. knots in the sequence or other bad 
clashes) that the optimization is unable to recover, and you may be able 
to manually tweak the initial model to correct this.

Unfortunately, Modeller does very little checking on a user-provided 
initial model, and expects it to match the .ini file (i.e. same residue 
and atom order, just with different coordinates). So you can get weird 
errors if this is not the case.

	Ben Webb, Modeller Caretaker
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