Thanks Paolo, Unfortunately the behaviour I described persists with SVN 4995.
cheers, Doug Quoting Paolo Tosco <paolo.to...@unito.it> on Thu, 30 Aug 2012 11:48:51 +0200: > Dear Douglas, > > did you try to use the SVN version? I myself submitted a number of > fixes to the pdbqt format module which might solve your header > issues (not the protonation problems, though). > > Cheers, > Paolo > > -- > ========================================================== > Paolo Tosco, Ph.D. > Department of Drug Science and Technology > Via Pietro Giuria, 9 - 10125 Torino (Italy) > Tel: +39 011 670 7680 | Mob: +39 348 5537206 > Fax: +39 011 670 7687 | E-mail: paolo.to...@unito.it > http://open3dqsar.org | http://open3dalign.org > ========================================================== > > > > On 30 Aug 2012, at 11:33, Douglas Houston > <dhous...@staffmail.ed.ac.uk> wrote: > >> Hi, >> >> I don't know if this is related, but I've found another example of >> what appears to be an "erroneous structure" with the -p option in >> 2.3.1. I noticed it when converting to PDBQT format, but there's >> also a problem when I convert to PDB. The files in question are >> attached. >> >> babel -isdf input.sdf -opdbqt nop.pdbqt >> #works fine (also works OK with -h option) >> >> babel -isdf input.sdf -opdbqt p.pdbqt -p 7.4 >> #produces a nonstandard PDBQT file with multiple header sections. >> Converting to PDB with -p also produces an erroneous structure but >> at least the file format is complied with (I think). >> >> I've noticed this problem with a number of molecules, all of which >> contain azide groups. >> >> cheers, >> >> Doug >> >> >> Quoting Noel O'Boyle <baoille...@gmail.com> on Wed, 22 Aug 2012 >> 15:28:11 +0100: >> >>> Just following up on this as Chris just fixed the issue reported by >>> Douglas. The problem in your case is different, if it is actually an >>> error by Open Babel. If you look in phmodel.txt, you can see all of >>> the protonation rules. The one being applied in your case is: >>> >>> #guanidine or amidine >>> TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* 12.5 >>> >>> If you don't like this, just comment it out by putting a # at the >>> start. Should we adjust the rule somehow as you think it is incorrect? >>> >>> Regards, >>> Noel >>> >>> On 18 June 2012 05:43, green69 <gcinci...@gmail.com> wrote: >>>> Hey Douglas, thank you for your help and for the information >>>> provided. I'll >>>> take this into account. >>>> >>>> I hope somebody could fix this bug soon. The '-p' option seems so >>>> useful to >>>> me. >>>> >>>> Cheers! >>>> >>>> -- >>>> View this message in context: >>>> http://forums.openbabel.org/erroneous-structures-when-the-option-p-is-activated-tp4655151p4655158.html >>>> Sent from the General discussion mailing list archive at Nabble.com. >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. Discussions >>>> will include endpoint security, mobile security and the latest in malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> OpenBabel-discuss mailing list >>>> OpenBabel-discuss@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >> >> >> >> >> _____________________________________________________ >> Dr. Douglas R. Houston >> Lecturer >> Room 3.23 >> Institute of Structural and Molecular Biology >> Michael Swann Building >> King's Buildings >> University of Edinburgh >> Edinburgh, EH9 3JR, UK >> Tel. 0131 650 7358 >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> <p.pdbqt> >> <nop.pdbqt> >> <input.sdf> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > _____________________________________________________ Dr. Douglas R. Houston Lecturer Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
