Re: [modeller_usage] dynamic memory allocation failed

[Modeller Caretaker <>]

Ilya Shlyakhter wrote:
> I'm getting a "dynamic memory allocation failed" message on a very
> small model. The test examples work fine, but when I modify
> model-full.py for my own use it gives a problem. Below I give the
> files I used, and the error message.  I would appreciate any
> suggestions.

I'm guessing that there was a typo in your message, and that really you 
had '*' as the sequence for 1yod, i.e.

> > P1;1yod
> structureX:1yod:1:B:51:B:phospholamban:Homo sapiens: 1.80:0 
> *

There is no residue 1 in chain B in PDB code 1yod, so Modeller fails to 
read in this sequence (notice that it's given as zero length):

> #  Code        #_Res #_Segm PDB_code    Name 
> -------------------------------------------------------------------------------
>  1       1fjk      52      1        1fjk phospholamban
>  2       1yod       0      0        1yod phospholamban

The final error message you got is, admittedly, rather cryptic, but I've 
just put in a more informative error (which will be in the next Modeller 
release).

The solution to your problem is to correct the start residue:chain for 
the 1yod sequence.

	Ben Webb, Modeller Caretaker
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