Bugs item #3324420, was opened at 2011-06-22 10:49 Message generated for change (Tracker Item Submitted) made by gcincilla You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3324420&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: File Translation Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: green69 (gcincilla) Assigned to: Nobody/Anonymous (nobody) Summary: openbabel move the position of already present hydrogens Initial Comment: Hi! I'm using openbabel v. 2.3.0 with a GNU/Linux OS (Ubuntu 10.10). I have the following problem on adding hydrogens with babel: I have a structure contaning only certain hydrogen atoms (in my case the "polar hydrogens" e.g. those bounded to etheroatoms) and I want to add (with the command "obabel -ipdb filename.pdb -p 7.5 -o -O filename_H.pdb") all the hydrogens present in the structure at pH = 7.5. It seems that babel first eliminate those hydrogens already present in the structure and then re-add all hydrogens atoms. This results in the change of the position of those hydrogens (in my case the polar ones) that were already present in the structure. I think this can lead to serious problem. I'll attach the 2 files and a figure where one can appreciate the difference in the hydroxy hydrogen position. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3324420&group_id=40728 ------------------------------------------------------------------------------ Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Data protection magic? Nope - It's vRanger. Get your free trial download today. http://p.sf.net/sfu/quest-sfdev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
