No dice. I killed "obabel 2GDZ.pdb -O 2GDZ.pdbqt -xr" after 4.5 mins. Presumably it should only take a few seconds max?
- Noel On 1 February 2011 14:49, Stuart Armstrong <stuart.armstr...@inhibox.com> wrote: > 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 > > ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
