On 19 July 2011 11:34, Martin Kamp Jensen <[email protected]> wrote: > On Tue, Jul 19, 2011 at 11:13 AM, Noel O'Boyle <[email protected]> wrote: >> >> 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. :-) > > I'm not an MD guy, I'm not even a biochemist. I'm just a computer scientist > trying to help biochemists :)
Even better of course. :-) > At least I now discovered that to make it work, you first have to read a PDB > file and convert it into an OBMol object. Then you can read an XTC for that > PDB into the same OBMol object and that object then contains all the > conformers. So I guess no patching is necessary. Maybe I just needed a line > or two of documentation to point my in the right direction. After getting it > to work I realize that it makes sense to have to read in a "full molecule" > first because the XTC only contains atom coordinates. Oh well :) It still looks like a bug. I don't know anything about the XTC format, but presumbly Open Babel should perceive the molecule structure from the coordinates as best it can. >> >> 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
