[Chimera-users] Problems open Amber trajectory

[Eric Pettersen]

Hi Oliver,
	Chimera doesn't handle unwrapped trajectories.  You will need to use  
the ptraj "image" command to prevent molecules from being split across  
box boundaries in your final trajectory.  Perhaps the other errors  
will not occur with the re-imaged trajectory.  If not, please let me  
know.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On Aug 19, 2009, at 4:15 AM, Koch, O (Oliver) wrote:

> Dear Chimera Team,
>
> I have a problem opening an AMBER trajectory using chimera v1.3  
> (2000/12/09).
>
> When I look at the frames, they show this "spider web" phenomenon:  
> Connections between atoms that should not be there.
> Furthermore, I got errors throughout the whole file: "Error: line  
> too long in:"
>
> I have a topology file and a coordinate file created using leap/ 
> ptraj from the Amber Tools 1.2.
> I could look at the files using vmd with the options "Amber 7 parm"  
> for the topology file and "Amber coordinates with periodic box" for  
> the coordinate file.
> Therefore, the files should not be corrupt, but, of course, I would  
> prefer to use Chimera for visualizing...
>
> Can you give me any advice how to open the files correctly?
>
> Thanks in advance.
>
> Kind regards,
> Oliver
>
> Dr. Oliver Koch
> BioChemInformatics Postdoctoral-Fellow
> Intervet Innovation GmbH
> Zur Propstei
> 55270 Schwabenheim, Germany
>
> E-Mail:   	oliver.koch at sp.intervet.com
> Phone:	+49 (6130) 948 396		
> Fax:	+49 (6130) 948 517		
>
> Home    	http://www.intervet.com
>
> Sitz der Gesellschaft: Schwabenheim 	     Amtsgericht Mainz, HRB 23  
> 166	  Geschäftsführer: Dr. Peter Schmid
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