Re: [AMBER] facing problem to create a prmtop file for oxonium cation

From: Hannes Loeffler <>
Date: Mon, 16 Mar 2015 10:32:25 +0000

I would think a (trialkyl) oxonium is outside the range of molecules
antechamber was designed for. You should probably also check if a AM1
Hamiltonian (used in the bcc charge method) is really appropriate for
your molecule.

On Mon, 16 Mar 2015 15:29:06 +0530
Sohag Biswas <> wrote:

> Dear amaber users,
> In attempt to create a topology file for oxonium cation from pdb file
> by following command, it is showing,
> For atom[1]:O1, the best APS is not zero, bonds involved by this atom
> are frozen
> The command line is
> antechamber -i eth.pdb -fi pdb -o eth.prepi -fo prepi -c bcc -nc 1
> -at gaff -pf y
> It will be very helpful for helping me. Many Many thanks to all. Here
> i am attaching also the pdb file which i created by xleap.

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Received on Mon Mar 16 2015 - 04:00:02 PDT
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