Re: [AMBER] leap duplicates bond ('triangular' bond) warning

From: Pietro Aronica <>
Date: Tue, 02 Apr 2019 20:45:04 +0800

Hello,From my experience, those warnings do not need any action. You might however get rid of them by specifying the hybridisation of the new atom types. If you open the leaprc file you use, at the very top there will be a list of atoms and the hybridisation for each (sp3, sp2, etc). Add your atom types and the warning should go away.Cheers Pietro 
-------- Original message --------From: Fabian Glaser <> Date: 02/04/2019 20:16 (GMT+08:00) To: AMBER Mailing List <> Cc: Fabian Glaser <> Subject: [AMBER] leap duplicates bond ('triangular' bond) warning Dear amber experts,I am trying to parametrize several antibiotics, now of course they are weird and have a double ring which produces some antechamber and parmcheck2 warnings, with several DIHE and IMPROPER warnings, file attache and tleap actually produces the prmtop file, although I am able to run MD without any apparent problem.But tleap gives the following warnings:/anaconda3/bin/teLeap: Note.1-4: angle 5579 5586 duplicates bond ('triangular' bond) or angle ('square' bond)/anaconda3/bin/teLeap: Note.1-4: angle 5578 5580 duplicates bond ('triangular' bond) or angle ('square' bond)So my questions are: Do this warnings need some action?If yes, what exactly they mean and what should try to do?I attach the parmchek2 .frcmod file, the leap.log file the pdb and the mol2 file I used to run everything. Thanks a lot!!Best,FabianFabian Glaser PhDHead of the Structural  Bioinformatics section Bioinformatics Knowledge Unit - BKUThe Lorry I. Lokey Interdisciplinary Center for Life Sciences and EngineeringTechnion - Israel Institute of Technology, Haifa, IsraelWeb +972 (0) 4 8293701_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Tue Apr 02 2019 - 06:00:03 PDT
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