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.molnar@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 <jmsstarlight@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
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