Hi,
I thank you all for your answers and all the help provided. I will try to
solve the problem with all the info I got and let you know the results.
Best regards,
Enrique
2018-06-13 10:20 GMT-05:00 Thomas Holder :
> Hi all,
>
> I made a pull request to Pymol-script-repo where oldnumeric is repl
Hi all,
I made a pull request to Pymol-script-repo where oldnumeric is replaced with
numpy in the bundled ADT copy. Anyone willing to review and test this?
https://github.com/Pymol-Scripts/Pymol-script-repo/pull/98
Cheers,
Thomas
> On Jun 13, 2018, at 11:24 AM, J.R. W wrote:
>
> Enrique,
Enrique,
I don’t know a lot about AutoDock, but I do know a lot about python. That error
comes from using a new versions of numpy (1.14) that does not have old numeric
with it anymore (deprecated in 1.9).
You can do a few things. Run the script within pymol which uses a earlier
release of n
Dear everyone,
I have recently installed the open-source Pymol 1.7.x on Ubuntu 16.04
sudo-apt-get install pymol
I then added the Pymol-script-repo which includes the Autodock/Vina plugin
and ADT. This has worked well for me in the past. However on this new
installation I keep getting the foll
Dear everyone,
I have recently installed the open-source Pymol 1.7.x on Ubuntu 16.04, I
also installed the AutoDock plugin and after some configuration it all
worked fine.
However, I then installed the GROMACS plugin as described in the PyMOL wiki
sudo add-apt-repository ppa:tomaszm/dynamics
su
Hello,
I've been working through different tabs of the AD plugin, trying to find
out what works with PyMOL v.1.7.1.3. The radio buttons on the grid tab are
not working, but the biggest hurdle I've come against to this point is on
the receptor tab. The plugin will correctly import the receptor file
Thomas,
Thanks for suggestions.
1)I have installed Numpy.
2) File "/usr/lib/python2.7/dist-packages/pymol/parser.py", line 260, in
parse
exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
File "", line 1, in
File "/usr/share/pyshared/pmg_tk/startup/autodock_plugin.py", line 62, i
Hi James,
is it recent version of PyMOL, or recent version of Windows which makes
trouble? On Windows, the plugin tries to write to the PyMOL installation
folder, which fails if you don't have write permissions there. This needs to be
fixed, the plugin should write to the users folder also on W
Dear PyMol users!
I've forced with the problem of the installation of AutoDock plugin
pymoawiki.org/index.php/Autodock_plugin in recent pymol version. I've
tried to install it manually from the downloaded py script but at the
starting of pymol below error has bbeen appeared
Unable to initialize
Hello all,
I have to perform virtual screening for which I installed the autodock
plugin in Pymol(1.2 evaluation versiom)[Python 2.5 and Numpy 1.3].
Configuration settings and grid box settings are fine, but i m facing
problems when it comes to accepting the receptor and the ligands.
e.g.- I got
Dear all,
I have a problem running autodock 4 using autodock plugin in pymol.
The pymol automatically shut down once I run the autogrid. I read the
webpage saying that I have to turn the feature off by setting the
environmental variable to ADPLUGIN_NO_OUTPUT_REDIRECT
I am not very famili
Hi,
no, I'm not planning to develop a solution without the dependency of
autodocktools.
The plugin is just a tool to use autodock and vina from within a pymol
session. The Autodocktools are used for receptor and ligand preparation which
is an essential part of a docking protocol, equally import
Hi,
On Tue, Feb 16, 2010 at 08:26:00PM +0100, Daniel Seeliger wrote:
> take a look into
> ~/.ADplugin/pymol_autodock_plugin.conf
> and set the path to the autodocktools scripts correctly. Then the plugin
> should find them.
Speaking of which, I was just taking a look about including your autodo
Hi Sing,
take a look into
~/.ADplugin/pymol_autodock_plugin.conf
and set the path to the autodocktools scripts correctly. Then the plugin
should find them.
Cheers,
Daniel
On Tuesday 16 February 2010 08:06:40 pm Kin Sing Stephen Lee wrote:
> Dear all,
>
> This is the first time for me to use t
Dear all,
This is the first time for me to use the autodock plugin and I have
some simple questions. I'm using Macbook Pro (OS X v 10.5 -
leopard). Autodock and autodock tools run fine in the X11 terminal.
In the autodock plugin, I need to put in the autodock tool program
path,so I put
@lists.sourceforge.net
> >
> > You can reach the person managing the list at
> >pymol-users-ow...@lists.sourceforge.net
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of PyMOL-users digest..."
> >
gt; Today's Topics:
>
> 1. Re: load dcd files problem (Hugo G. de Teran)
> 2. pymol autodock plugin (Daniel Seeliger)
> 3. movie.roll in middle of movie (Benjamin Bobay)
> 4. Re: movie.roll in middle of movie (Warren DeLano)
> 5. Grid View of a Group (T. Andrew Binkow
tone [mailto:jedg...@mit.edu]
> > Sent: Thursday, August 13, 2009 1:34 PM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] pymol autodock plugin
> >
> > The autodock plugin written by Daniel Seeliger ceased to function
>
> (load)
>
> >
August 13, 2009 1:34 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] pymol autodock plugin
>
> The autodock plugin written by Daniel Seeliger ceased to function
(load)
> when I upgraded to Pymol 1.2r1.
> Although it is not compatible directly with Autodock 4, it did have
The autodock plugin written by Daniel Seeliger ceased to function (load) when I
upgraded to Pymol 1.2r1.
Although it is not compatible directly with Autodock 4, it did have the useful
functionality of
presenting an autodock 'box' that was readily tweakable, so that the parameters
could be expo
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