Hi, I am trying to add hydrogens to the approved.sdf list from drugbank, babel gives several warnings but it works on it. See below the output. I then feed the approved_hyd_filter.sdf as is to the rosie ligand docking engine, which gives me a failure, which I suspect it is related to babel errors:
molfile_to_params step failed, please double check your input files! I would appreciate any suggestion to how solved this problem. Best regards, Fabian Here is the ouptut of applying babel to the approved.sdf I can ->babel -isdf approved.sdf -osdf approved_hyd_filter.sdf -h -p 7 ============================== *** Open Babel Warning in Expand Alias R was not chemically interpreted ============================== *** Open Babel Warning in Expand Alias R was not chemically interpreted 1556 molecules converted 4 warnings 70419 audit log messages [fabian@Fabians-iMac:/Users/fabian/PROTOCOLS/docking/drugbank]% -> ____________________ Dr. Fabian Glaser Head of the Structural Bioinformatics section Bioinformatics Knowledge Unit - BKU fgla...@technion.ac.il Tel: +972 4 8293701 http://bku.technion.ac.il The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
