Bugs item #2912360, was opened at 2009-12-10 16:15 Message generated for change (Tracker Item Submitted) made by goodsell You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2912360&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: Command-line Tools Group: 2.2.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: david goodsell (goodsell) Assigned to: Nobody/Anonymous (nobody) Summary: trouble with guanidinium Initial Comment: I've been using version 2.2.3 (Dec 1 09) on Linux to add hydrogens to a series of small molecules. It is working beautifully except for guanidinium and amidinium groups. In most cases, it treats these as uncharged, and I can't get the pH flag to make changes. Here is an odd example that shows a change in behavior: PDB entry 1dwc--the ligand from the file is called MIT. If I extract the ligand (attached here) and add hydrogens, the guanidinium comes out fine, and the pH function seems to work (the carboxyl gets protonated at low pH, and the guanidium becomes uncharged at high pH). Then, delete the two oxygens in the carboxyl group (O33 and O34). With that modified file, the guanidinium is always treated as uncharged, at all pH values that I tried. I find this same behavior with almost all other files with guanidinium groups (for instance, ligand from pdb files: 1bmm, 1bmn, 1bra, 1dwb, etc). Thanks for your help! David Goodsell goods...@scripps.edu ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=2912360&group_id=40728 ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
