[AMBER] Wrong connectivity after antechamber/Gaussian16

From: Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de>
Date: Fri, 27 Oct 2017 20:19:04 +0200

Hi all,

I am trying to parametrize a ligand with antechamber and G16. However
the connectivity of my molecule is not as desired after running:

antechamber -i IL3.mol2 -fi mol2 -o IL3.com -fo gcrt -gv 1 -ge IL3.gesp
-at gaff2


antechamber -i IL3.gesp -fi gesp -o IL3_resp.mol2 -fo mol2 -c resp -eq 2
-at gaff2

Specifically, a proton moves from a nitrogen to an oxygen, leading to a
COOH and NH2 instead of the desired COO- and NH3+.

Is there a command to restrain the gaussian geometry optimization?



M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Tel.: +49 89 2180 77059
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Received on Fri Oct 27 2017 - 11:30:03 PDT
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