Hi all
I've been trying to install apbs to use this new plugin, as I imagine a
lot of people will want to. I run into a problem in the compilation
which I wonder if anyone can help with. [I know this is not strictly a
Pymol question but given the general interest perhaps I can be excused.
There seems to be a glitch with the apbs-users list too - my help awaits
moderation which I know can take days]
Anyway, after installation of the prerequisite MALOC (rpm or compiled,
makes no difference) I get the following when trying to configure for
apbs compilation
-- begin configuring for MALOC linkage
checking for FETK_INCLUDE... yes
checking for FETK_LIBRARY... yes
checking maloc/maloc.h usability... yes
checking maloc/maloc.h presence... yes
checking for maloc/maloc.h... yes
checking for maloc_link in -lmaloc... no
configure: error: MALOC libraries or headers missing: exiting on error!
I saw some messages about libraries during compilation of maloc. I
don't known if they have anything to do with the apbs compilation
problem but I added /usr/local/lib/i686-pc-linux to /etc/ld.so.conf and
did a /sbin/ldconfig and it didn't help.
Any advice much appreciated
Daniel
On Wed, 2004-07-14 at 16:37, Michael George Lerner wrote:
Hi all,
APBS (http://agave.wustl.edu/apbs/) is a package that allows you to
perform very fast, accurate electrostatics calculations. I've written a
PyMOL plugin that allows you to run APBS and visualize the results very
easily from within PyMOL (version 0.96 or higher).
The plugin lets you configure all of the normal APBS parameters (whether
you want the full nonlinear Poisson-Boltzmann equation or not, what the
various dielectrics should be, ion concentrations, etc.).
Also, the plugin comes with a visualization tab that can be used to aid in
the visualization of any electrostatic potential.
It's quite easy to install, thanks to PyMOL's new plugin system.
Anyway, you can find the plugin on my webpage
http://www.umich.edu/~mlerner/PyMOL/
or directly from
http://www.umich.edu/~mlerner/PyMOL/apbs_tools.py
drop it into pymol/modules/pmg_tk/startup/ and you're ready to go.
Please let me know if you find this useful and/or have any questions or
comments!
-michael
Here are the directions, taken from http://www.umich.edu/~mlerner/PyMOL/
This is a PyMOL plugin which lets you run APBS from within PyMOL.
To install it,
1. Make sure you have PyMOL version 0.96 or higher.
2. Download a copy of apbs_tools.py and place it in
pymol/modules/pmg_tk/startup/.
Now, you'll see APBS Tools... under the Plugins menu. This plugin allows
fairly complete configuration of APBS, but it's very easy to set up a
standard electrostatic potential calculation:
1. Load your molecule into PyMOL
2. Load the plugin
3. Click on Set grid
4. Click on Run APBS
5. Use the plugin's Visualization tab to look at the results
This will use PyMOL's new ability to assign AMBER charges and radii. If
you wish to use your own externally-generated PQR file, you can set that
up on the plugin's main page.
The plugin should auto-detect the location of the APBS binary on your
system, but you can set it manually under the APBS Location tab.
My plugin can calculate appropriate grid lengths and spacings. It ensures
that the grid spacing is 0.5A or finer. If you have APBS's psize.py
installed and you wish to use it, you can set that up on the plugin's
APBS Location tab.
Finally, it's worth noting that the plugin's Visualization tab can be
used for easy visualization of any electrostatic potential, not just
things generated by APBS.
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
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