[apbs-users] Trouble installing Pdb2pqr with propka

[Ashalatha Sreshty]

Hello Users,

I need help with installation of pdb2pqr and apbs, as I intend to perform calculations on protein, ligands and protein-ligand complexes. For this , I had to compile with propka.

Despite of trying the installation as described in the install.md, I get the following error " Failed building pdb2pka/substruct/Algorithms.so: Error 1". I have also installed numpy in Python 2.7 and used that python executable to compile pdb2pqr.

I will be very grateful, if any of you can help me in this by underscoring the installation problem.

(BTW, I am installing on linux OS (Redhat 6.2))

The following is the output generated upon executing the below command.

Please help

/home/asha/WORK/ASHA/Programs/Python-2.7/bin/python scons/scons.py

scons: Reading SConscript files ...
not using opal
scons: done reading SConscript files.
scons: Building targets ...
scons: `pdb2pqr.py' is up to date.
scons: `apbs_cgi.cgi' is up to date.
scons: `visualize.cgi' is up to date.
scons: `querystatus.cgi' is up to date.
scons: `src/aconf.py' is up to date.
scons: `html/server.html' is up to date.
Copy("pdb2pqr.cgi", "pdb2pqr.py")
g++ -o pdb2pka/substruct/Algorithms.so -shared pdb2pka/substruct/Algorithms.os -L/home/asha/WORK/ASHA/Programs/Python-2.7/lib -lpython2.7
/usr/bin/ld: /home/asha/WORK/ASHA/Programs/Python-2.7/lib/libpython2.7.a(cobject.o): relocation R_X86_64_32S against `PyCObject_Type' can not be used when making a shared object; recompile with -fPIC
/home/asha/WORK/ASHA/Programs/Python-2.7/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
scons: *** [pdb2pka/substruct/Algorithms.so] Error 1
scons: building terminated because of errors.

TARGETS: ['pdb2pqr.py', 'apbs_cgi.cgi', 'visualize.cgi', 'querystatus.cgi', 'src/aconf.py', 'html/server.html', 'pdb2pqr.cgi', 'pdb2pka/substruct/Algorithms.so', 'pdb2pka/_pMC_mult.so']

========================
Configuration Parameters
========================

Version: master
Install directory: /home/asha/pdb2pqr/
pdb2pka and ligand support: True
Path to the website directory: http://localhost.localdomain/pdb2pqr/
PDB2PQR jobs run via the web interface will be forked on the server.

The preferred way to configure the build is by editing the file build_config.py

Run scons with the python that you intend to use with pdb2pqr.
For example: "/opt/bin/python scons/scons.py" will setup pdb2pqr to be run with /opt/bin/python

Run "python scons/scons.py install" to install pdb2pqr in /home/asha/pdb2pqr/

Run "python scons/scons.py basic-test" for a basic functionality test
Run "python scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.
Run "python scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.
Run "python scons/scons.py pdb2pka-test" for a simple test of PDB2PKA functionality.
    Requires numpy, PDB2PKA support compiled AND the APBS python libraries compiled and installed in the pdb2pka directory.

To setup a web service create a symbolic link to /home/asha/pdb2pqr/ that enables you to view http://localhost.localdomain/pdb2pqr/ after running "scons/scons.py install"

Run "python scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.
VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.
The resulting projects will need to modified to use VS natively to compile the code or debug.

FAILED!!!!
Failed building pdb2pka/substruct/Algorithms.so: Error 1

--

Dr. M. Asha Latha Sreshty,
Post doctoral Fellow,
Prof. Surolia's Research Group,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore - 560012.

[Monson, Kyle E]

Hi!

 

Our build scripts are supposed to detect if the -fPIC flag is needed but apparently that doesn’t always seem to work out. I’ve attached  two updated build script files that will help you work around the problem. They will allow you to add arbitrary compile flags to the build. Just drop them into the pdb2pqr directory, overwriting what is there. Then in the build_config.py file uncomment the line

 

#EXTRA_CXXFLAGS="-fPIC"

 

And that will force the -fPIC option into the compile.

 

Let me know if you have any problems.

 

Kyle

Run "python scons/sconspy pdb2pka-test" for a simple test of PDB2PKA functionality.

    Requires numpy, PDB2PKA support compiled AND the APBS python libraries compiled and installed in the pdb2pka directory.

To setup a web service create a symbolic link to /home/asha/pdb2pqr/ that enables you to view http://localhost.localdomain/pdb2pqr/ after running "scons/scons.py install"

Run "python scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.
VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.
The resulting projects will need to modified to use VS natively to compile the code or debug.

FAILED!!!!
Failed building pdb2pka/substruct/Algorithms.so: Error 1