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, DougQuoting 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.htmlSent 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
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p.pdbqt
Description: Binary data
nop.pdbqt
Description: Binary data
input.sdf
Description: Binary data
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