[Chimera-users] Problems open Amber trajectory

Koch, O (Oliver) oliver.koch at sp.intervet.com
Wed Aug 19 04:15:42 PDT 2009

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,

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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