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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