We really could do with a MD guy on the team. Hint hint. It might just take a few minutes to patch up xtcformat.cpp. Nudge nudge. :-)
On 18 July 2011 13:50, Martin Kamp Jensen <[email protected]> wrote: > Hello, > I am trying to read an XTC file generated by GROMACS with no luck. > > From the command line, >> >> obabel path/totraj.xtc -O test.pdb > > results in >> >> *** Open Babel Warning in OpenBabel::XTCFormat::ReadMolecule >> Error: number of atoms in the trajectory (X) doesn't match the number of >> atoms in the supplied molecule (0). >> 0 molecules converted > > where X is the actual number of atoms in the molecules of the trajectory (I > tried two different trajectory with no luck). > It also does not work using code (which is the way I would like it to work, > using the command line above was just a test): > >> OBConversion conversion = new OBConversion(); >> conversion.SetInFormat("xtc"); >> OBMol molecule = new OBMol(); >> conversion.ReadFile(molecule, "path/to/traj.xtc"); >> System.out.println(molecule.NumConformers()); // Prints 0, should print >> 1001 according to gmxcheck -f path/to/traj.xtc > > Regards, > Martin. > ------------------------------------------------------------------------------ > AppSumo Presents a FREE Video for the SourceForge Community by Eric > Ries, the creator of the Lean Startup Methodology on "Lean Startup > Secrets Revealed." This video shows you how to validate your ideas, > optimize your ideas and identify your business strategy. > http://p.sf.net/sfu/appsumosfdev2dev > _______________________________________________ > OpenBabel-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ Magic Quadrant for Content-Aware Data Loss Prevention Research study explores the data loss prevention market. Includes in-depth analysis on the changes within the DLP market, and the criteria used to evaluate the strengths and weaknesses of these DLP solutions. http://www.accelacomm.com/jaw/sfnl/114/51385063/ _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
