On 2013-04-09 03:28, Marcus D. Hanwell wrote: > Hi, > > We are using obabel to perform geometry optimizations etc on the > command line, and we are hitting a bug that seems to only present > itself on the Mac. If the input and output formats are the same then > the operation fails, for example, > > obabel -icml -ocml --minimize --log --ff UFF > > That is using standard in/out, but it also seems to happen when using > files. This works as expected on Linux and Windows, are we diverging > from expected use too much or is this a bug. This is the same in 2.3.2 > and master, using 10.6.8 and GCC 4.2.1. > > The full output is below, compared with using xyz as the output (we > could of course work around this issue by using different formats). > There is a SMARTS error I just noticed too, but that seems unrelated > to this bug on the Mac. > > $ obabel -icml ethane.cml -ocml --minimize --log --ff UFF > ============================== > *** Open Babel Error in RegisterOptionParam > The number of parameters needed by option "t" in The LPMD file > format. differs from an earlier registration. > ============================== > *** Open Babel Error in SMARTSError > SMARTS Error: > [#6+:1](~N:2)(~N:3)* > ^ > > > A T O M T Y P E S > > IDX TYPE RING > 1 H_ NO > 2 C_3 NO > 3 H_ NO > 4 H_ NO > 5 C_3 NO > 6 H_ NO > 7 H_ NO > 8 H_ NO > > S E T T I N G U P C A L C U L A T I O N S > > SETTING UP BOND CALCULATIONS... > SETTING UP ANGLE CALCULATIONS... > SETTING UP TORSION CALCULATIONS... > SETTING UP OOP CALCULATIONS... > SETTING UP VAN DER WAALS CALCULATIONS... > > C O N J U G A T E G R A D I E N T S > > STEPS = 2500 > > STEP n E(n) E(n-1) > -------------------------------- > 1 2.378 4.699 > 4 1.069 1.069 > CONJUGATE GRADIENTS HAS CONVERGED > 0 molecules converted > > $ obabel -icml ethane.cml -oxyz --minimize --log --ff UFF > ============================== > *** Open Babel Error in RegisterOptionParam > The number of parameters needed by option "t" in The LPMD file > format. differs from an earlier registration. > ============================== > *** Open Babel Error in SMARTSError > SMARTS Error: > [#6+:1](~N:2)(~N:3)* > ^ > > > A T O M T Y P E S > > IDX TYPE RING > 1 H_ NO > 2 C_3 NO > 3 H_ NO > 4 H_ NO > 5 C_3 NO > 6 H_ NO > 7 H_ NO > 8 H_ NO > > S E T T I N G U P C A L C U L A T I O N S > > SETTING UP BOND CALCULATIONS... > SETTING UP ANGLE CALCULATIONS... > SETTING UP TORSION CALCULATIONS... > SETTING UP OOP CALCULATIONS... > SETTING UP VAN DER WAALS CALCULATIONS... > > C O N J U G A T E G R A D I E N T S > > STEPS = 2500 > > STEP n E(n) E(n-1) > -------------------------------- > 1 2.378 4.699 > 4 1.069 1.069 > CONJUGATE GRADIENTS HAS CONVERGED > 8 > Ethane > H 1.17997 -0.00310 1.00769 > C 0.76583 -0.02288 -0.02125 > H 1.16144 0.85024 -0.57962 > H 1.10906 -0.95033 -0.52388 > C -0.76582 0.02291 0.02127 > H -1.16141 -0.85054 0.57913 > H -1.10918 0.95009 0.52435 > H -1.17989 0.00361 -1.00770 > 1 molecule converted > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > Interesting, it seems to be something with writing cml. I'm using trunk but I get: [artemisia:~/tmp] % obabel -isdf ethanol.sdf -ocml ethanol.cml ============================== *** Open Babel Error in OpenAndSetFormat Cannot open ethanol.cml
and then all the output is dumped on the terminal instead (it does do the minimization as requested). So it seems something goes wrong opening a cml file for writing. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
