I have X11 and developer tools. I can get maloc installed, but when I
configure apbs, I get:
checking build system type... powerpc-apple-darwin7.5.0
checking host system type... powerpc-apple-darwin7.5.0
...
...
checking if Fortran 77 compiler accepts -nofor_main... no
checking how f77 mangles function names... configure: error: failed to
compile fortran test program
I also notice that the same place that has APBS has this site that
computes electrostatics from a PDB file and returns a PQR file. This
would be lovely for people like me to use for the calculations. Now
how can I use the PQR file to create an electrostatic surface with
pymol?
Ann
Ann Mullin
Research Scientist
Cell and Molecular Biology Dept.
Tulane University
New Orleans, LA 70118-5698
504-865-6742 (Ph)
504-865-6785 (FAX)
amul...@tulane.edu
On Sep 1, 2004, at 5:26 PM, Alex W. Smith wrote:
Ann:
The first question is do you have the Apple X11 and Developer tools
installed. If you don't you will have to get them installed before
you do anything. If you have them installed then the directions below
should help out.
I just got through doing all this for my G4 AlPB. Turns out I need
more memory but everything works fine. It may seem like a lot at
first but installing from source (especially on a OS X box) is
probably the best bet. I tried the binary for G4 and had some library
problems. Below are two links that helped me a lot. The first is
directions for installing from source. Be sure to get the MALOC (link
is on the first webpage) tar file as well as the APBS. Start out with
the Installation directories. Be sure to list the directory name
properly (i.e. change export FETK_SRC=/home/soft/src to the
directories you want to install to.
Then just move both tar files to the /home/soft/src (or whatever you
call it) directory. Then just follow the directions for MALOC.
For APBS, just follow the directions for unpacking APBS. Then follow
Bill Scott's tweak (http://chips.csb.ki.se/pymol/msg02192.html). It
should not take that long to compile them both.
Once APBS is installed you can use the plugin to find the binary,
which will be in the apbs/bin directory.
Don't let the source code install scare you. They are easy enough to
beat after a bit.
Hope this helps.
Alex
http://agave.wustl.edu/apbs/doc/html/user-guide/x122.html
http://chips.csb.ki.se/pymol/msg02192.html
On Sep 1, 2004, at 2:12 PM, Ann Mullin wrote:
Hi,
All I want to do is be able to create an electrostatic surface
representation of a simple molecule.
I am seriously overwhelmed by the information for compiling and
setting APBS on their website. I was happy to fine a link to
download a package with an installer, but when I run it it fails at
the very end and tells me to try installing again. Also, is there
any place that I should be installing this? I tried in the
Applications folder and in the folder I made to surround PyMOL and
it's user manual.
I also notice that there is a binary ready to use for G5 on the
website, but where do I put this to work, and where is the psize.py
file. I rarely work on a UNIX platform and I have a very hard time
switching from macOS to UNIX and back, since macOS is almost all
point and click.
Thanks for any help. Ann
Ann Mullin
Research Scientist
Cell and Molecular Biology Dept.
Tulane University
New Orleans, LA 70118-5698
504-865-6742 (Ph)
504-865-6785 (FAX)
amul...@tulane.edu
