File Format Support item #3192996, was opened at 2011-02-25 22:45 Message generated for change (Tracker Item Submitted) made by fgrun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=447448&aid=3192996&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Output Group: None Status: Open Priority: 5 Private: No Submitted By: Felix Grun (fgrun) Assigned to: Nobody/Anonymous (nobody) Summary: PDBQT format - compatibility with PyRx (Vina) and PaDEL-ADV Initial Comment: Conversion error for PDBQT output ?? Conversion of files containing ligand SMILES structures --> .mol --> .mol2 --> .pdbqt using Open Babel 2.3.0 or iBabel 3.0(beta) results in PDBQT formatted files that cannot be read by various Vina GUI programs for high throughput screening (various parsing errors). The problem appears to lie in the final PDBQT conversion since mol2 files can be used as inputs in ADT, PyRx or Raccoon to generate the appropriate PDBQT formatting. A comparison of the two types of files shows that: Babel 2.3.0 produces PDBQT output files which replace lines marked as REMARK with USER (for ligand names etc), ATOM with HETATM and end with TER. Replacing USER with REMARKS and removing TER allows files to be correctly read. Is this updated file syntax being adopted as the standard PDBQT format or is it a platform dependent version produced by InhibOx ? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=447448&aid=3192996&group_id=40728 ------------------------------------------------------------------------------ Free Software Download: Index, Search & Analyze Logs and other IT data in Real-Time with Splunk. Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
