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Re: [Adun-users] Adun Michael Johnston Thu Feb 02 01:00:27 2012

Pdbmodifier is not a real plugin and should be there automatically.

Addhydrogens is in the adunplugins.xcodeprj and needs to be built
separately - just noticed this isn't written anywhere for mac. Install
all the stable plugins in one go by running

xcodebuild -target Meta -configuration Release

In XCodeProjects/

however are you aware the plugins will not appear in the list until
you load a structure into the builder?

On 6 Jan 2012, at 16:44, deepak kumar <[EMAIL PROTECTED]> wrote:

> Hi,
>
> In the installed version of Adun on mac. The gui lacks "add hydrogen and
> pdbmodifier" components.How to add missing plugins on mac installed adun?
>
> cheers.
>
> On Fri, Jan 6, 2012 at 2:00 PM, deepak kumar <[EMAIL PROTECTED]>wrote:
>
>> Hi,
>>
>> After running the simulation on the system (2rrbsystem.dataosurce,
>> H2O.datasource, template.temp) , I got these files ( AdunCore.errors
>> AdunCore.log  objectData  Template  Trajectory0).Plz, see the attachment.
>> and on running resultconverter on energy mode, I get the files (.csv) as in
>> attachment which are empty, also on running the configuration mode no files
>> are obtained. The command line looks like this:
>>
>> All attached files are in the mac_2rrb folder attached.
>>
>> [EMAIL PROTECTED] SimulationOutput]$ ResultsConverter -Mode Energy
>> -Simulation mac_2rrb_simulation.simulation/
>> Processing Arguments
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg Output
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg Trajectory
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg Subsystems
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg Start
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg Length
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg StepSize
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg Terms
>> 2012-01-06 13:17:10.794 ResultsConverter[3636] Optional arg Unit
>> 2012-01-06 13:17:10.828 ResultsConverter[3636] Encoded data path and
>> current location are not equal
>> 2012-01-06 13:17:10.828 ResultsConverter[3636] Substituting stored data
>> path with current location
>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation/
>> 2012-01-06 13:17:10.828 ResultsConverter[3636] Stored URL is
>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation/
>> GSCBufferString
>> 2012-01-06 13:17:10.828 ResultsConverter[3636] Decode data URL
>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation/
>> and path
>> /cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation
>> Accessing Results
>> Validating Arguments against Results
>> 2012-01-06 13:17:11.058 ResultsConverter[3636] Unable to load plugin at
>> /home/deepak/adun/Plugins/Analysis/TransitionPathED
>> Performing Conversion
>> Complete
>> [EMAIL PROTECTED] SimulationOutput]$ ls
>> 2rrbsystem-H2OContainerInteractionResults.csv  2rrbsystemResults.csv
>> H2OContainerResults.csv  mac_2rrb_simulation.simulation
>>
>> [EMAIL PROTECTED] SimulationOutput]$ ResultsConverter -Mode
>> Configuration -Simulation mac_2rrb_simulation.simulation/
>> Processing Arguments
>> 2012-01-06 13:17:40.029 ResultsConverter[3643] Optional arg Trajectory
>> 2012-01-06 13:17:40.030 ResultsConverter[3643] Optional arg Subsystems
>> 2012-01-06 13:17:40.030 ResultsConverter[3643] Optional arg Start
>> 2012-01-06 13:17:40.030 ResultsConverter[3643] Optional arg Length
>> 2012-01-06 13:17:40.030 ResultsConverter[3643] Optional arg StepSize
>> 2012-01-06 13:17:40.041 ResultsConverter[3643] Encoded data path and
>> current location are not equal
>> 2012-01-06 13:17:40.041 ResultsConverter[3643] Substituting stored data
>> path with current location
>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation/
>> 2012-01-06 13:17:40.041 ResultsConverter[3643] Stored URL is
>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation/
>> GSCBufferString
>> 2012-01-06 13:17:40.041 ResultsConverter[3643] Decode data URL
>> file://localhost/cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation/
>> and path
>> /cbbl/users/deepak/simulations/mac_2rrb/SimulationOutput/mac_2rrb_simulation.simulation
>> Accessing Results
>> Validating Arguments against Results
>> 2012-01-06 13:17:40.180 ResultsConverter[3643] Unable to load plugin at
>> /home/deepak/adun/Plugins/Analysis/TransitionPathED
>> Performing Conversion
>> 2012-01-06 13:17:40.186 ResultsConverter[3643]     No dynamics for
>> H2OContainer
>> 2012-01-06 13:17:40.187 ResultsConverter[3643]     No dynamics for
>> 2rrbsystem
>> Complete
>>
>> Plz have a look.
>>
>>
>> cheers.
>>
>>
>> On Thu, Jan 5, 2012 at 8:59 PM, Jordi Villà i Freixa <
>> [EMAIL PROTECTED]> wrote:
>>
>>> Miguel, Alfons, could you take pelargonium out of the CBBL queue?
>>>
>>>
>>> Begin forwarded message:
>>>
>>> *From: *Nils Jan Daniel Drechsel <[EMAIL PROTECTED]>
>>> *Date: *January 5, 2012 7:27:37 PM GMT+01:00
>>> *To: *deepak kumar <[EMAIL PROTECTED]>
>>> *Cc: [EMAIL PROTECTED]
>>> *Subject: **Re: [Adun-users] Adun*
>>>
>>> this has been solved. It is due to the fact that the job was executed on
>>> the machine pelargonium, which is running a different version of fedora.
>>> We
>>> need to take it out of the cbbl queue as adun will not run there.
>>>
>>> On Thu, Jan 5, 2012 at 7:20 PM, deepak kumar <[EMAIL PROTECTED]
>>>> wrote:
>>>
>>> Hi,
>>>
>>>
>>> I ran the test simulation on Mac. Was able to create the simulation. when
>>>
>>> submitted it to run i got this error in the "stderr.txt" file:
>>>
>>>
>>> AdunCore: error while loading shared libraries: libbfd-2.17.50.0.18-1.so:
>>>
>>> cannot open shared object file: No such file or directory
>>>
>>>
>>>
>>> Could you help. attached below are the datasource and template files.
>>>
>>>
>>>
>>> cheers.
>>>
>>>
>>> On Thu, Jan 5, 2012 at 11:13 AM, Jordi Villà i Freixa <
>>>
>>> [EMAIL PROTECTED]> wrote:
>>>
>>>
>>> try to follow Michael's advice.
>>>
>>> uninstall 0.26 version for gnustep-startup and install 0.25 using the
>>>
>>> same
>>>
>>> instructions than before http://lavandula.imim.es/adun-new/?page_id=1400
>>>
>>>
>>> Begin forwarded message:
>>>
>>>
>>> *From: *Michael Johnston <[EMAIL PROTECTED]>
>>>
>>> *Date: *January 5, 2012 11:00:54 AM GMT+01:00
>>>
>>> *To: *César Ávila <[EMAIL PROTECTED]>
>>>
>>> *Cc: *Jordi Villà i Freixa <[EMAIL PROTECTED]>,
>>>
>>> [EMAIL PROTECTED]
>>>
>>> *Subject: **Re: [Adun-users] Adun*
>>>
>>>
>>> The last gnustep-startup that worked reliably for me was 0.25 - I use
>>>
>>> this
>>>
>>> to build the packages for Fedora/Suse and these worked normally when I
>>>
>>> tested them. As Cesar mentioned use the guidelines on this page -
>>>
>>> http://lavandula.imim.es/adun-new/?page_id=186 - to work out what
>>>
>>> gnustep
>>>
>>> library versions to use.
>>>
>>>
>>> Post this sartup versionthere are a number of changes in gnustep to
>>>
>>> support the apples new objective-c runtime (OSX 10.5 compatible) the
>>>
>>> effect
>>>
>>> of which is to break AdunShell.
>>>
>>>
>>> Also FYI there is some problem between the latest Cairo  (an underlying
>>>
>>> graphical library) on ubuntu and the latest gui which stops the Adun from
>>>
>>> starting (not sure if this problem exists on other distros - the fact
>>>
>>> that
>>>
>>> the gui opens for deepak with 0.26 suggests not).
>>>
>>>
>>> As Cesar said if you can send along the log files (specifically UL.log)
>>>
>>> after you observe the problem we can work from there.
>>>
>>>
>>> 2012/1/4 César Ávila <[EMAIL PROTECTED]>
>>>
>>>
>>> I've seen a lot of errors with the gui using gnustep version other than
>>>
>>> the
>>>
>>> one posted in
>>>
>>> http://lavandula.imim.es/adun-new/?page_id=186
>>>
>>> **
>>>
>>> I personally prefer gnustep startup 0.20.1 (it works for me).
>>>
>>>
>>>
>>>
>>> 2012/1/4 Jordi Villà i Freixa <[EMAIL PROTECTED]>
>>>
>>>
>>> Deepak uses an adun version obtained following the steps in
>>>
>>> http://lavandula.imim.es/adun-new/?page_id=1400
>>>
>>>
>>> On Jan 4, 2012, at 6:55 PM, César Ávila wrote:
>>>
>>>
>>> Hi Deepak and welcome to Adun.
>>>
>>> As Nils mentioned, some problems might arise with the GUI related to
>>>
>>> the
>>>
>>> GNUStep version that you have installed on your system.
>>>
>>> Can you provide more information about this? I think it might also
>>>
>>> come
>>>
>>> helpful any error messages that you receive in
>>>
>>> ~/adun/UL.log and ~/adun/AdunServer.log
>>>
>>> Cheers
>>>
>>> Cesar
>>>
>>>
>>> 2012/1/4 Nils Jan Daniel Drechsel <[EMAIL PROTECTED]>
>>>
>>>
>>> Just to add something,
>>>
>>>
>>> Deepak is working in the linux version of the GUI. I've never had
>>>
>>> these
>>>
>>> problems in the mac version, so I think it might be GNUstep
>>>
>>> related?
>>>
>>>
>>> On Wed, Jan 4, 2012 at 4:34 PM, deepak kumar <
>>>
>>> [EMAIL PROTECTED]
>>>
>>> wrote:
>>>
>>>
>>> Hi all,
>>>
>>>
>>> I am a new user of Adun. While working with it I came across some
>>>
>>> problems,
>>>
>>> as below:
>>>
>>>
>>> a) I am trying to create a system. After creating the system and
>>>
>>> saving
>>>
>>> it,
>>>
>>> nothing appears at the database ([EMAIL PROTECTED]) in the
>>>
>>> "systems" of
>>>
>>> GUI.
>>>
>>> b) If i try to rename the system from "none" to some desired name
>>>
>>> the
>>>
>>> tool
>>>
>>> hangs and the system is not renamed. When trying to remove/cut/...
>>>
>>> use
>>>
>>> any
>>>
>>> of the "edit" options, it does not work.
>>>
>>>
>>> Could you plz let me know how can i resolve these problems.
>>>
>>>
>>>
>>>
>>> cheers.
>>>
>>>
>>> --
>>>
>>> Deepak Kumar
>>>
>>>
>>> Computational Biochemistry and Biophysics lab
>>>
>>> Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
>>>
>>> Parc de Recerca Biomèdica de Barcelona
>>>
>>> C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>>>
>>>
>>>
>>>
>>> Phone: +48 66 46 82950
>>>
>>> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <
>>>
>>> [EMAIL PROTECTED]
>>>
>>> %20>
>>>
>>>
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>>>
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>>>
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>>>
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>>>
>>> team
>>>
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>>>
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>>>
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>>>
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>>>
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>>>
>>>
>>>
>>> --
>>>
>>> Jordi Villà i Freixa
>>>
>>> Computational Biochemistry and Biophysics lab
>>>
>>> Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
>>>
>>> Parc de Recerca Biomèdica de Barcelona
>>>
>>> C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>>>
>>> Tel: +34 93 316 0504 // Fax: +34 93 316 0550
>>>
>>> e-mail: [EMAIL PROTECTED]
>>>
>>> http://cbbl.imim.es
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> Deepak Kumar
>>>
>>> Bioinformatics Laboratory
>>>
>>> Institute of Molecular Biology and Biotechnology
>>>
>>> Adam Mickiewicz University
>>>
>>> Umultowska 89, 61-614 Poznan, Poland
>>>
>>>
>>> Phone: +48 66 46 82950
>>>
>>> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]>
>>>
>>>
>>>
>>> This message has been automatically forwarded to you by the Adun team
>>>
>>> http://adun.imim.es
>>>
>>> _______________________________________________
>>>
>>> Adun-users mailing list
>>>
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>>>
>>> https://mail.gna.org/listinfo/adun-users
>>>
>>>
>>>
>>>
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>>>
>>>
>>>
>>
>>
>> --
>> Deepak Kumar
>> Bioinformatics Laboratory
>> Institute of Molecular Biology and Biotechnology
>> Adam Mickiewicz University
>> Umultowska 89, 61-614 Poznan, Poland
>>
>> Phone: +48 66 46 82950
>> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]>
>>
>
>
>
> --
> Deepak Kumar
> Bioinformatics Laboratory
> Institute of Molecular Biology and Biotechnology
> Adam Mickiewicz University
> Umultowska 89, 61-614 Poznan, Poland
>
> Phone: +48 66 46 82950
> E-mail: [EMAIL PROTECTED] , [EMAIL PROTECTED] <[EMAIL PROTECTED]>
>
> This message has been automatically forwarded to you by the Adun team 
> http://adun.imim.es
> _______________________________________________
> Adun-users mailing list
> [EMAIL PROTECTED]
> https://mail.gna.org/listinfo/adun-users


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