Dear Noel,
Have you tried running it with the -xr option? It sounds like it's trying to
construct the torsion tree, which would take a huge amount of time for a
protein. With 'r' it should output rigidly.
Let me know if this helps,
Stuart
On 28 January 2011 14:42, Noel O'Boyle <baoille...@gmail.com> wrote:
> Hi all,
>
> I've just been trying to prepare a protein for setting up a docking
> with Autodock. Is this pdbqt format intended for this or is it just
> for the ligands? The description in the help message is somewhat
> minimal.
>
> In any case, I tried to do this conversion but after several minutes
> waiting I terminated it and filed a bug:
>
> https://sourceforge.net/tracker/?func=detail&aid=3167053&group_id=40728&atid=428740
> .
>
> Am I doing something wrong?
>
> - Noel
>
> On 1 September 2010 14:52, Stuart Armstrong
> <stuart.armstr...@inhibox.com> wrote:
> > Dear Open Babel,
> > Included here is the pdbqtformat.cpp file, which has read and write
> > capabilities. The help message (babel -Hpdbqt) gives the options and
> reads:
> > pdbqt Autodock Protein Data Bank Q (Partial Charge) & Type
> > Read Options e.g. -ab, -abd
> > b Disable automatic bonding
> > d Input file is in dlg (docking log file) format.
> > Write options, e.g. -xr, -xp, -xrp
> > b Enables automatic bonding before writing to pdbqt format
> > r Outputs rigid molecule (no branches)
> > s Outputs as a flexible residue
> > p Preserves the atom indexes from the input file (default is to
> renumber
> > sequentially).
> >
> > Specification at:
> >
> http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
> > ------------------------------
> >
> > The file makes use of atom and bond indexes, as its method involves
> deleting
> > atoms and bonds one at a time and counting the remaining pieces; this is
> > done by copying the molecule and operating on the copy, with the indexes
> > used to identify the relevant components in the original molecule object.
> > Tomorrow I should be able to send you a message confirming that you are
> free
> > to distribute the file (let me know if you require anything more).
> > All the best,
> > Stuart
>
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