From: Nuno Sousa Cerqueira (nscerque_at_fc.up.pt)
Date: Mon Nov 30 2009 - 18:35:39 CST

Hi Justin,

Thanks for the reply.
I have just realized what was happening.
I am using a mac to create the script. In the mac system ( mac intel)
the script was running ok, without any problems.
The error was occurring when I was running the same script in centOs.

I now found that the problem was due to a problem related to the text
file encoding.
I am using eclipse to develop the script, and in the mac system it
uses the text file encoding Mac Roman as the default. When I change it
to UTF-8 the script started to work fine in centOs, like it works on
MAc system.

So the problem is now solved.

cheers,

Nuno

On Nov 30, 2009, at 10:35 PM, Justin Gullingsrud wrote:

> Nuno,
>
> Did you get this figured out? If not, could you post the Tcl command
> you used? The timekeys file is a file that should be found at
> hA0A1a_DESfep01_solvent_10_lambda2_trj/timekeys, assuming the
> trajectory was created properly and managed to write at least one
> frame. Could you post the contents of that directory as well?
>
> Cheers,
> Justin
>
>
> On Thu, Nov 26, 2009 at 3:16 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>> Hi,
>> I'm not sure what might cause the error you're getting,
>> the best thing would be for you to contact the Desmond team
>> as they developed the dtrplugin for VMD. If you aren't able to
>> get into contact with them, let me know and I can ask the people
>> I know if they can answer this question.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Nov 26, 2009 at 05:53:58PM +0000, Nuno Sousa Cerqueira wrote:
>>> I am having the following error while running a tcl script that
>>> loads
>>> desmond trajectory into VMD:
>>>
>>> Info) Finished with coordinate file hA0A1a_DESfep01_solvent_10-out/
>>> fep1/hA0A1a_DESfep01_solvent_10_lambda2/
>>> hA0A1a_DESfep01_solvent_10_lambda2-out.cms.
>>> Info) Analyzing structure ...
>>> Info) Atoms: 2287
>>> Info) Bonds: 1536
>>> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
>>> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0
>>> Impropertypes: 0
>>> Info) Residues: 754
>>> Info) Waters: 752
>>> Info) Segments: 3
>>> Info) Fragments: 754 Protein: 1 Nucleic: 0
>>> Could not find timekeys file at /timekeys
>>> ERROR) Could not read file hA0A1a_DESfep01_solvent_10-out/fep1/
>>> hA0A1a_DESfep01_solvent_10_lambda2/
>>> hA0A1a_DESfep01_solvent_10_lambda2_trj/clickme.dtr
>>> Unable to load file 'hA0A1a_DESfep01_solvent_10-out/fep1/
>>> hA0A1a_DESfep01_solvent_10_lambda2/
>>> hA0A1a_DESfep01_solvent_10_lambda2_trj/clickme.dtr' using file type
>>> 'dtr'.
>>> Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
>>>
>>>
>>> Does anyone has an idea what , the ERROR : Could not find timekeys
>>> file at /timekeys, means ?
>>>
>>> Regards,
>>>
>>> Nscerqueira
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>
>
>
>
> --
> I speak of certain afternoons in early fall, waterfalls of
> immaterial gold, the transformation of the world, when everything
> loses its body, everything is held in suspense,
> and the light thinks, and each one of us feels himself thought by
> that reflective light, and for one long moment time dissolves, we are
> air once more...
> -- Octavio Paz, "I speak of the city"