Re: [modeller_usage] Error when using dope_loopmodel

[Modeller Caretaker <>]

Florian Odronitz wrote:
...
> Please note that I used the dope_loopmodel class instead of loopmodel  
> as indicated in the manual.
> When I run the script, it exits with the following message:
...
> check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity).
>                The objective function can thus not be calculated.
>
> Using dopehr_loopmodel gives the same error whereas the "old"  
> loopmodel works.
> Here is the Atom record from the PDB file:
>
> 	ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294
>
> The coordinates do not seem to be out of range. I also put a blank in  
> the middle ("1.00 103.06") to avoid problems with the parser, but to  
> no avail.

The error refers to the current set of coordinates (during optimization) 
- not the initial PDB coordinates. And don't put a blank into the PDB 
file - PDB files are fixed-column format, so it doesn't matter that 
there's no space between 1.00 and 103.06 (in fact, your "fixed" PDB file 
is now invalid).

An atomic coordinate at infinity is usually a symptom of large forces in 
your system. These can occur if you have a bad initial model (e.g. two 
atoms superposed or very close). It is more likely to occur with DOPE 
loop modeling than regular loop modeling since the former includes 
GB/SA. (The loop modeling potentials themselves, while they are 
atomistic pair potentials, plateau as r tends to 0, unlike electrostatic 
potentials which tend to infinity.)

> Am I doing something wrong here or is this a bug?

Could be either. You can try a different initial model if your initial 
model is very bad. Otherwise, send me your input files and I'll try to 
reproduce your problem, to determine whether it's a bug in the GB/SA code.

	Ben Webb, Modeller Caretaker
--
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