[Chimera-users] Error in viewing trajectories

Eric Pettersen pett at cgl.ucsf.edu
Mon Nov 28 11:17:42 PST 2011

Hi George,
	Support for the prmtop format used by AmberTools 1.5 was added since  
the Chimera 1.5.3 release, therefore you need to download the 1.6  
daily build to read your trajectory.


P.S.  Thanks for making your trajectory available.  That made it very  
easy to determine the problem.

                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Nov 28, 2011, at 11:01 AM, George Tzotzos wrote:

> Hi Elaine,
> Many thanks for this. Unfortunately the files are too big to email  
> them.  I'd be grateful if you and/or your colleagues could download  
> them from the following link.
> http://dl.dropbox.com/u/50952643/2erb-IND-traj.zip
> I'm using Chimera version 1.5.3 (build 33475).  My operating system  
> is OSX 1.6.8 on a 2x2.93 GHz 6-Core Intel Xeon machine.
> Many thanks in advance for all the help.
> George
> On Nov 28, 2011, at 6:24 PM, Elaine Meng wrote:
>> Hi George,
>> The better approach to report Chimera problems is with Help...  
>> Report a bug in the menu, or this web form.
>> <http://www.cgl.ucsf.edu/cgi-bin/chimera_bug_report_2.py>
>> It will let you attach a file (and include your email address if  
>> you want feedback).
>> In this case the trajectory file would be more useful than the  
>> error message.  Also, I guess we would need both prmtop and  
>> trajectory, and I'm not sure if the approach above would let you  
>> attach both, so yet another possibility is to send email to chimera-bugs at cgl.ucsf.edu 
>>  and attach both those files.  Please also mention your Chimera  
>> version and what kind of computer you are using (e.g. Windows,  
>> Mac ...).
>> Thanks,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On Nov 28, 2011, at 2:37 AM, George Tzotzos wrote:
>>> Yesterday I posted a message regarding Chimera issuing error  
>>> messages on trying to open trajectory files.
>>> The error was "TypeError: Attempt to form duplicate covalent bond."
>>> I believe that the problem arises from the fact that in preparing  
>>> the topology files with ANTECHAMBER (tleap) in AMBER, I generated  
>>> disulfide bonds. My guess is that the problem lies there. Has  
>>> anyone observed similar behaviour?
>>> Best regards
>>> George
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                         Eric Pettersen
                         UCSF Computer Graphics Lab

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