[Chimera-users] index out of range

[Eric Pettersen]

Hi Francesco,
	The problem is that Chimera 1.6.1 can't handle prmtop files generated  
by Amber 12.  You need to use the current daily build of Chimera.   
This problem would also be fixed if we made a 1.6.2 release, but it  
looks like we're going to make a 1.7 release (eventually) instead.

--Eric

On Jun 4, 2012, at 2:54 PM, Eric Pettersen wrote:

> 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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>
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