Editing Talk:APBS (section)

==Running with APBS 1.3 not working==
Well, I tried making the plugin run with APBS 1.3 and this is what I got:
  Running:
  prog=/usr/local/apbs-1.3-mac-univ/bin/apbs
  args=('/usr/local/apbs-1.3-mac-univ/bin/apbs', '--version')
  Results were:
  Return value: -5
  Output:
  dyld: Library not loaded: /usr/local/lib/x86_64/libgomp.1.dylib
    Referenced from: /usr/local/apbs-1.3-mac-univ/bin/apbs
    Reason: image not found
  Skipping /usr/local/apbs-1.3-mac-univ/bin/apbs because it appears to be broken (dyld)

Just wondering if you get the same. --[[User:Rendereason|Rendereason]] 16:36, 29 October 2010 (UTC)

I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)

The installation guide says:
"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
I have tried setting the variable ${APBS_PREFIX} to /usr/local/apbs-.13-mac-univ.
I've added these to my .zshrc but none of it works
  APBS_PREFIX=/usr/local/apbs-1.3-mac-univ/
  APBS_BINARY_DIR=/usr/local/apbs-1.3-mac-univ/bin/
  APBS_PSIZE_DIR=/usr/local/apbs-1.3-mac-univ/share/tools/manip/
  export APBS_PREFIX
  export APBS_BINARY_DIR
  export APBS_PSIZE_DIR
None of this had any effect on the unmodified apbsplugin.py. (When parameters set to ''None'')
Changing the parameters within apbsplugin.py to their desired folders gives the error above.
--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner|michael]] 19:40, 29 October 2010 (UTC)

Yes. Those errors happen with the pre-release version you posted. It also ignores the binary I have configured it to use in /usr/local/apbs/bin/ for the fink one in /sw64/bin/. 
 Also, I get this problem when running the plugin:
  GENERATING PQR FILE via PDB2PQR
  Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
  Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
  TESTING
  DONE TESTING
  Appended /sw64
  Unexpected error encountered while trying to import pdb2pqr: (<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr.pdb2pqr',), <traceback object at 0x116714908>)
  In show error 2
  Could not generate PDB2PQR file.  _generatePdb2pqrPqrFile failed.
  Could not generate PQR file!
--[[User:Rendereason|Rendereason]] 22:48, 4 November 2010 (UTC)

OK, I think I know what's causing at least some of the problems. I find email a lot easier than wiki pages for sorting all of this out. Can you send a list of the current errors you're getting along with your PyMOL version, APBS version, PDB2PQR version and operating system to me at my gmail account (mglerner)? Thanks! --[[User:Mglerner|michael]] 00:43, 5 November 2010 (UTC)