Re: [rDock-list-def] mol2 format

[Markus M. <me...@gm...>]

Dear Markus and Peter:
Apologies for the delay!

Here is an example:
I downloaded 1oyt for rcsb.org and processed it within maestro using the
prep wizard.
And the ligand is also attached. I exported this ligand in mol format from
maestro and converted it via obabel to sdf.

According to the manual rdock reads the atom name, cart cords and tripos
atom types. So all the other info is discarded?
Otherwise may be the numbering of the residues in the ATOM section is
different.

Best,
Markus

On Tue, Sep 24, 2019 at 8:26 AM Peter Schmidtke <pet...@gm...>
wrote:

> Hey Markus,
>
> any chance you can share the faulty mol2 files?
> I personally use open babel to do that.
>
> ++
>
> Peter
>
> > On 21 Sep 2019, at 01:00, Markus Metz <me...@gm...> wrote:
> >
> > Hello all:
> > I am trying to convert my protein to mol2 format and I have tried the
> following:
> > a) converted via maestro
> > b) used openbabel
> > c) used chimera
> > d) visually tried to pinpoint where my mol2 file differs from tutorial
> examples.
> >
> > In every case I failed to run the rbcavity command.
> > The best error message I am getting is
> > 'Corrupted MOL2 file: not enough fields in SUBSTRUCTURE'.
> >
> > I can find no difference between the tutorial example and the mol2 file
> created.
> > Of course rbcavity works with the tutorial files.
> >
> > How are you performing the mol2 conversion?
> > Kindly let me know,
> > Markus
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>
>