On Tue, Jul 19, 2011 at 12:43 PM, Noel O'Boyle <[email protected]> wrote:
> 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.
>
The XTC format [1] (almost) only contains Cartesian coordinates of atoms.
That is, no information about atom types, bonds, etc. is included. Hence, it
makes sense (at least to me) that you need a "reference molecule" with all
that information. Then by combining the "reference molecule" with a
trajectory for that molecule (the XTC file) you get an OBMol with as many
confomers as the number of frames in the trajectory.
What I think is needed is some documentation. Well, at least these mails are
now available if others get in trouble using an XTC file...
[1] http://www.psc.edu/general/software/packages/gromacs/online/xtc.html
>
> >>
> >> 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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> >> >
> >
> >
>
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