[Chimera-users] Error in viewing trajectories

[Eric Pettersen]

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.

--Eric

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

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


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
                         http://www.cgl.ucsf.edu


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