I am unable to convert adequately (using the OpenBabel::OBConversion method in
my own-program) the following standard PDB ligand to the MOL2 format on my
Win32 machine.
REMARK THIS IS THE LIGAND FROM 1stp.pdb
HETATM 903 C11 BTN A 300 9.051 4.576 -14.459 1.00 21.57 C
HETATM 904 O11 BTN A 300 8.147 5.373 -14.172 1.00 21.65 O
HETATM 905 O12 BTN A 300 8.697 3.498 -15.132 1.00 22.67 O
HETATM 906 C10 BTN A 300 10.321 4.413 -13.702 1.00 20.77 C
HETATM 907 C9 BTN A 300 10.215 3.247 -12.658 1.00 20.09 C
HETATM 908 C8 BTN A 300 11.487 2.972 -11.964 1.00 19.24 C
HETATM 909 C7 BTN A 300 11.627 1.558 -11.402 1.00 18.33 C
HETATM 910 C2 BTN A 300 10.923 1.086 -10.195 1.00 17.74 C
HETATM 911 S1 BTN A 300 10.884 2.103 -8.662 1.00 16.59 S
HETATM 912 C6 BTN A 300 10.299 0.620 -7.760 1.00 17.06 C
HETATM 913 C5 BTN A 300 11.142 -0.543 -8.274 1.00 17.47 C
HETATM 914 N1 BTN A 300 12.443 -0.631 -7.613 1.00 17.73 N
HETATM 915 C3 BTN A 300 13.467 -0.443 -8.453 1.00 17.95 C
HETATM 916 O3 BTN A 300 14.692 -0.446 -8.205 1.00 17.93 O
HETATM 917 N2 BTN A 300 12.974 -0.237 -9.695 1.00 17.92 N
HETATM 918 C4 BTN A 300 11.513 -0.265 -9.727 1.00 17.65 C
CONECT 903 904 905 906
CONECT 904 903
CONECT 905 903
CONECT 906 903 907
CONECT 907 906 908
CONECT 908 907 909
CONECT 909 908 910
CONECT 910 909 911 918
CONECT 911 910 912
CONECT 912 911 913
CONECT 913 912 914 918
CONECT 914 913 915
CONECT 915 914 916 917
CONECT 916 915
CONECT 917 915 918
CONECT 918 910 913 917
END
Here are the errors in the output that comes out of it:
===========================
*** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Error 1.
Cannot initialize database
===========================
*** Open Babel Warning in OpenBabel::OBTypeTable::Translate
Error 2.
Cannot perform atom type translation: table cannot find requested types.
===========================
OpenBabel :: converted 1 molecule
The error 2 comes out multiple times.
The PDB file is indeed converted.
I am also able to do the same conversion using the same sources on my Linux or
MacOSX machines.
However there are some odd SYBYL atom types in the MOL2 format in the Win32
version:
C3, Cac, Nam, C2... where all of those do appear as C.3, ?? Cac ??, N.am, C.2
on my Linux/MacOS machines.
I updated the latest sources using svn (revision 5061) and recompiled the whole
Visual Studio solution using VS10.
The solution was generated using the default_build.bat file in the
windows-vc2008 folder.
So, I do have the latest openbabel-2.dll version.
When compiliing my application, I did link to openbabel-2.lib (the latest).
I copied all required files (more than I needed I suppose) in the same folder
as my application:
openbabel-2.dll
formats_*.obf files
plugin_*.obf files
and the following libraries:
zlib1.dll (version 1.2.3.0)
xdr-0.dll
libxml2.dll
libinchi.dll (version 1.0.4.1)
libpng14-14.dll
libfontconfig-1.dll
libexpat-1.dll
iconv.dll (version 1.9.0.0)
libcairo-2.dll
freetype6.dll
Thank you all for your answers.
Francis Gaudreault
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