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 :)
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 :)
>
> 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.
> >
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