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
