Hi Stephen,
you should try lattest CAVER which could be downloaded from
http://www.caver.cz
before installing it via Pymol plugin menu, you should to open
caver-3.0-1.py and find here
CAVER3_LOCATION = "directory/where/caver3/is/located"
and modify this on your path providing it to the jar file directly ( in
this version there is no jar path in pymol plugin itself).
Does anyone use it for the analysis of the ligand sites? I've test it with
the GPCR and found 3 possible pathways. I'n not sure how It have been
clustered but now I'n looking for the method for the steered MD along
caver-predicted pathes
James
2013/11/17 Stephen P. Molnar <s.mol...@sbcglobal.net>
> I would be interested in just how the problem has been solved!
>
> I just installed caver v-2.1.2 in the 64 bit Debian Testing with PyMOL
> v-1.6.0.0 compiled from the latest svn and functioning perfectly on my
> system.
>
> Carver installed from the PyMOL wicki via the PyMOL Plugin Manager without
> any complaints. Yet when I try to use the plugin I get:
>
> ERROR: Directory incorrectly specified -plugin.jar not found, check
> directory/where/jar/with/plugin/is/locate/Carver2_1.jar
>
> Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup subdirectory.
> Also other plugins are working without complaint.
>
> This is exactly the way the plug was working the last time that I
> attempted its installation and use.
>
>
> On 11/15/2013 03:14 PM, James Starlight wrote:
>
> This issue have been solved. Caver works fine. Does anyone tried to
> include path information obtained by caver to the NAMD steered md
> simulation? I'm looking for the protocol for guiding namd forces along the
> direction obtaned from CAVER.
>
>
> James
>
>
> 2013/11/15 James Starlight <jmsstarli...@gmail.com>
>
>> Dear Pymol Users!
>>
>>
>> In the latest 3.0 releases of the CAVER plugin lack the source path for
>> the caver.jar launch file. Could you tell me how I could define this path
>> manually from pymol shell? I've try to make calculations with thus plugin
>> having Caver 3.0 dir in the work folder but obtained error that
>> /where/caver3 not found
>>
>>
>> Thanks for help
>>
>> James
>>
>
>
>
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> --
> Stephen P. Molnar, Ph.D. Life is a fuzzy set
> Foundation for Chemistry Stochastic and
> multivariatewww.FoundationForChemistry.com
> (614)312-7528 (c)
> Skype: smolnar1
>
>
>
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