[AMBER] Aromatic bonds disappear during sdf creation with sleap

From: Guenegou, Guillaume [ORDFR] <GGUENEGO.ITS.JNJ.com>
Date: Wed, 27 Jul 2011 14:28:37 +0200

Dear all,

Versions : Amber11/AmberTools 1.5

I use sleap in order to convert a mol2 file into a sdf file.

My input file looks like this :
source leaprc.ff03.r1
source leaprc.gaff
molecule = loadmol2 molecule.mol2
savesdf molecule molecule.sdf

My mol2 file contains aromatic bonds. But, surprise, the sdf file does
not contain anymore aromatic bonds.
I tried several viewers and the problem remains. Double bonds are still
there but aromatic bonds became single bond.

Is this a bug or is there anything I am doing wrong?


Ps : Dr Case, I did not forget to try the mol2 features patch you send
me but I was in holidays and now I have to wait the IT coordinator to
patch Amber. Hope we can do that in the 2 next weeks.

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Received on Wed Jul 27 2011 - 05:30:05 PDT
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