[AMBER] geometry of amino

From: Song Hu <Song.hu.GHDDI.org>
Date: Tue, 14 Apr 2020 05:59:00 +0000


I tried a simulation with a ligand like, the red N should be sp2, so the amino group should be a plane, but during the simulation, I extract one snapshot, it was not a plane, why?

I prepared the ligand with command line: antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc; parmchk2 -i ligand.mol2 -f mol2 -o ligand.frcmod -a y

Do you have any idea why the amino was not a plane?

Thank you for the help!

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Received on Mon Apr 13 2020 - 23:00:02 PDT
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