Re: [AMBER] Parametrization of Small Molecules

From: David A Case <>
Date: Fri, 18 May 2018 07:58:13 -0400

On Fri, May 18, 2018, Johannes Loeffler wrote:
> I am trying to parametrize small molecules for free energy calculations.
> However, in the antechamber step the atoms in the resulting mol2 file
> are renamed and reordered. The command I used:
> antechamber -i 13a.log -fi gout -o 13_test.mol2 -fo mol2 -c resp -a
> 13a.pdb -ao pdb -at gaff -nc 1 -rn 13a
> Is there a reason why antechamber does not take the names from the
> specified pdb file, or is there something wrong with my command?

The -ao flag takes an "additional file operation", whereas the -fa flag
takes an additional file format. So you want something like this:

   .... -a 13a.pdb -fa pdb -ao name ....

(Untested, but this is what "antechamber -help" indicates should be


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Received on Fri May 18 2018 - 05:00:03 PDT
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