Compiling smina on ARM architecture
Scoring and Minimization with AutoDock Vina
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Hello,
I am currently working on compiling smina on a Raspberry Pi 4 v1.2. I installed all the dependencies listed in the readme. Downloaded and compiled OpenBabel 3.1.1 from source (because only 2.4 is in the repository), ran Cmake and then compiled with it with make. As it got to the end to link the libsmina.a library to the smina executable, I got these errors regarding OpenBabel.
[ 97%] Linking CXX executable smina
/usr/bin/ld: libsmina.a(molgetter.cpp.o): in function
MolGetter::readMoleculeIntoModel(model&)': molgetter.cpp:(.text+0x694): undefined reference toOpenBabel::OBMol::StripSalts(unsigned int)'/usr/bin/ld: libsmina.a(SminaConverter.cpp.o): in function
SminaConverter::MCMolConverter::MCMolConverter(OpenBabel::OBMol&)': SminaConverter.cpp:(.text+0x480): undefined reference toOpenBabel::OBMol::SetConformer(unsigned int)'/usr/bin/ld: libsmina.a(SminaConverter.cpp.o): in function
SminaConverter::MCMolConverter::convertConformer(unsigned int, std::ostream&)': SminaConverter.cpp:(.text+0xb88): undefined reference toOpenBabel::OBMol::SetConformer(unsigned int)'/usr/bin/ld: libsmina.a(PDBQTUtilities.cpp.o): in function
IsRotBond_PDBQT(OpenBabel::OBBond*, unsigned int)': PDBQTUtilities.cpp:(.text+0xc4): undefined reference toOpenBabel::OBAtom::GetHvyDegree() const'/usr/bin/ld: PDBQTUtilities.cpp:(.text+0x104): undefined reference to
OpenBabel::OBAtom::GetHvyDegree() const' /usr/bin/ld: libsmina.a(PDBQTUtilities.cpp.o): in functionOutputAtom(OpenBabel::OBAtom, context&, std::vector<openbabel::obatom*, std::allocator<openbabel::obatom*=""> >&, parsing_struct&, unsigned int, unsigned int)':PDBQTUtilities.cpp:(.text+0x264): undefined reference to
OpenBabel::OBElements::GetSymbol(unsigned int)' /usr/bin/ld: PDBQTUtilities.cpp:(.text+0x338): undefined reference toOpenBabel::OBElements::GetSymbol(unsigned int)'/usr/bin/ld: PDBQTUtilities.cpp:(.text+0x35c): undefined reference to
OpenBabel::OBElements::GetSymbol(unsigned int)' /usr/bin/ld: libsmina.a(PDBQTUtilities.cpp.o): in functioncreateSDFContext(OpenBabel::OBMol&, std::vector<openbabel::obatom*, std::allocator<openbabel::obatom*=""> >, sdfcontext&)':PDBQTUtilities.cpp:(.text+0x14b8): undefined reference to `OpenBabel::OBElements::GetSymbol(unsigned int)'
collect2: error: ld returned 1 exit status
make[2]: [CMakeFiles/smina.dir/build.make:97: smina] Error 1
make[1]: [CMakeFiles/Makefile2:105: CMakeFiles/smina.dir/all] Error 2
make: </openbabel::obatom*,></openbabel::obatom*,>** [Makefile:84: all] Error 2
What is going on with the OpenBabel definitions that is making it error out in the last step?
If it helps.
OS: Raspberry Pi OS Lite - March 4th, 2021
Compiler: gcc (Raspbian 8.3.0-6+rpi1) 8.3.0
Thanks.
Do you have multiple versions of openbabel installed? My guess is the headers it is compiling with do not match the library it is trying to link with.
Yes I do. I had originally downloaded the package from the repository and found out when running CMake to prepare everything that it was the incorrect version.
UPDATE: I uninstalled OpenBabel 2.4 from the Raspberry Pi and it compiled and worked just fine. Thanks for the help.