the file is in the /src folder

the plugin gui should automatically scan to find the binaries for the plugin.  

you can also run pdq2pqr locally on the mac too (instead of using the server) and use it with the apbs plugin prior to ‘set the grid’ 

open terminal and run
fink install pdb2pqr
this takes a long time also

Good luck!

university of cincinnati
On Nov 13, 2013, at 10:38 AM, Baker, Nathan <> wrote:

Hi Sarah –
I’m adding Keith Fligg to this email to see if he can work with Andrew to help fix the problem.
Thank you,
Nathan Baker
Laboratory Fellow
Pacific Northwest National Laboratory
From: Sarah Witzke [] 
Sent: Tuesday, November 12, 2013 12:03 PM
Cc: Baker, Nathan; Aaron Oakley;; Stevens, Andrew J (PNNL)
Subject: Re: [apbs-users] running apbs on OS X 10.8
Dear all,
I am having the same problems as Aaron when I try to install APBS on OS 10.8.5.
Instead i downloaded the code from the git tree as suggested by Andrew.
I followed the steps in the file "buildWith", but for the lines "cp -r build/x86_64-unknown-linux-gnu/include/ ." and "cp -r build/x86_64-unknown-linux-gnu/lib/ ." I replaced "unknown-linux-gnu" with "apple-darwin12.5.0".
Then "cd ../build" and cmake -DENABLE_FETK=YES -DBUILD_SHARED_LIBS=YES ..
This produced an error about not being able to extract contrib/tabibp - which makes sense, since tabibp is not included in the "contrib" folder.
I downloaded the tabipb code myself and put tabipb.exe in contrib/tabibp
Then I ran the cmake command again, which this time ran smoothly (except not installing the openmpi, which I do not need) - the last couple of lines of output is:
-- -L/Users/witzke/apbs_test/apbs-code/lib -lapbs_geoflow;-lm;-L/Users/witzke/apbs_test/apbs-code/lib -L/opt/local/lib/gcc47 -lgfortran -ltabipb;-lmaloc;-lstdc++;-L/Users/witzke/apbs_test/apbs-code/fetk/lib;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lblas;-lvf2c;-ltetgen;-ltriangle;-lg2c;-lreadline apbs_generic;apbs_pmgc;apbs_mg;apbs_geoflow;apbs_fem
-- -std=c99
-- Supplemental tools enabled
-- Building mesh
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem
-- Building manip
-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/witzke/apbs_test/apbs-code/build
Unfortunately however, when I type "make" I get this:
[  6%] Performing configure step for 'tabipb'
CMake Error: The source directory "/Users/witzke/apbs_test/apbs-code/build/tabipb-prefix/src/tabipb" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.
make[2]: *** [tabipb-prefix/src/tabipb-stamp/tabipb-configure] Error 1
make[1]: *** [CMakeFiles/tabipb.dir/all] Error 2
make: *** [all] Error 2
I am not very good with compiling/installation/etc and I apologize if I have made stupid mistakes or should have known better, but I have spent very long time and am completely stuck now.
Any help is greatly appreciated.
Kind regards,
Sarah Witzke 

Den lørdag den 17. august 2013 01.54.22 UTC+2 skrev Stevens, Andrew J (PNNL):
Hi Aaron,
What build system are you using (Xcode or gcc version)?
You can also try compiling the git repository version instead of the release version: 
But it will take some time to download.
From: <Baker>, Nathan Baker <>
Date: Thursday, 15 August 2013 1928
To: Aaron Oakley <>
Cc: "" <>, Andrew Stevens <>
Subject: Re: [apbs-users] running apbs on OS X 10.8
Hi Aaron,
I'm sorry about the problems you've experienced. Andrew, can you please help?

On Aug 15, 2013, at 18:26, "Aaron Oakley" <> wrote:

Hi all,
I just installed the latest distribution of APBS for OS X (APBS-1.4-osx).
On the first attempt to execute I got:
dyld: Library not loaded: libmaloc.dylib
  Referenced from: /usr/local/APBS-1.4-osx/bin/apbs
  Reason: image not found
Trace/BPT trap: 5 I updated the DYLD_LIBRARY_PATH environmental variable to include /usr/local/APBS-1.4-osx/lib
Now I get:
dyld: Library not loaded: /usr/lib/libmpi_cxx.0.dylib
  Referenced from: /usr/local/APBS-1.4-osx/bin/apbs
  Reason: image not found
Trace/BPT trap: 5
Any help appreciated.
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