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

From: Fabian Glaser <fabian.glaser.gmail.com>
Date: Tue, 2 Apr 2019 15:16:39 +0300

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!!



Fabian Glaser PhD

Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web http://bku.technion.ac.il/
Tel +972 (0) 4 8293701
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Received on Tue Apr 02 2019 - 05:30:01 PDT
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