[Chimera-users] index out of range

[Eric Pettersen]

Hi Francesco,
	I have seen this error reported a couple of times, but the reports  
were anonymous and I couldn't do much to solve the problem.  Anyway,  
this error indicates that there are residues in the structure that  
have no atoms(!).  Not an ideal situation.  If you could send me your  
PSF file (or prmtop if that's what you're using) and part of your DCD,  
that would help me debug this.
	If you can't send them by mail, let me know and I'll set up FTP.

--Eric

On Jun 3, 2012, at 10:13 AM, Francesco Pietra wrote:

> Running movie for prmtop/dcd proved extremely slow at amd64, finally
> showing the protein in a water box, albeit offering very limited
> analysis. Error message: index out of range, error processing "monitor
> changes". The log is 16MB!, below the startr and end of the log:
>
> MDTools 1.2 Exp (2005-08-20) by James Phillips.
> Trajectory.DCD.MDToolsMarch97.md.help() for more info.
> HomoCoord 1.3 Exp (2005-08-20)
> - Constants 1.1 Exp (2004-05-17)
> - AtomGroup 1.4 Exp (2007-02-07)
> - local 1.1 Exp (2004-05-17)
> Unknown OSTYPE ??? set.  Viewing and plotting are disabled.
> - Trans 1.2 Exp (2005-08-20)
> - DCD 1.10 Exp (2007-02-07)
> - Data 1.2 Exp (2005-08-20)
> using memory mapping
> REMARKS FILENAME=./heat-01.dcd CREATED BY NAMD
> REMARKS DATE: 06/03/12 CREATED BY USER: francesco
> Model 0 (heat-01.dcd) appears to be a protein without secondary
> structure assignments.
> Automatically computing assignments using 'ksdssp' and parameter  
> values:
>  energy cutoff -0.5
>  minimum helix length 3
>  minimum strand length 3
> Use command 'help ksdssp' for more information.
> Traceback (most recent call last):
>  File "/usr/local/chimera_Nov3.2011/share/chimera/triggerSet.py",
> line 83, in invoke
>    self._funcData, triggerData)
>  File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line
> 1161, in _cacheCheck
>    if len(kids) == molecule.rootForAtom(kids[0],
> IndexError: list index out of range
> Error processing trigger "monitor changes":
>
> ....................................
> ....................................
>
> Traceback (most recent call last):
>  File "/usr/local/chimera_Nov3.2011/share/chimera/triggerSet.py",
> line 83, in invoke
>    self._funcData, triggerData)
>  File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line
> 1161, in _cacheCheck
>    if len(kids) == molecule.rootForAtom(kids[0],
> IndexError: list index out of range
> Error processing trigger "monitor changes":
> IndexError: list index out of range
>
>  File "/usr/local/chimera_Nov3.2011/share/chimera/Sequence.py", line
> 1161, in _cacheCheck
>    if len(kids) == molecule.rootForAtom(kids[0],
>
> See reply log for Python traceback.
>
> Thanks for the attention
> francesco pietra
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