-O ethanol.cml On 9 April 2013 00:20, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > 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
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