Re: [AMBER] Wrong connectivity after antechamber/Gaussian16

From: David A Case <>
Date: Fri, 27 Oct 2017 15:20:59 -0400

On Fri, Oct 27, 2017, Andreas Tosstorff wrote:
> 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 -fo gcrt -gv 1 -ge IL3.gesp
> -at gaff2
> and
> 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?

Sure: edit the file to remove the "opt" option from the route card,
before running the Gaussian calculation. That will mean that you will use
the starting configuration, so you will want to make sure that the geometry
in the IL3.mol2 file is reasonable.


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Received on Fri Oct 27 2017 - 12:30:03 PDT
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