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

From: David A Case <>
Date: Mon, 16 Mar 2015 07:47:41 -0400

On Mon, Mar 16, 2015, Sohag Biswas wrote:
> 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

To add to what Hannes said: the message above is just for information, and is
not an error.

As with all antechamber output, you should treat the resulting force field
with care: it is often just a first pass. In this case, look carefully at the
atom types and parameters associated with atom O1.


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Received on Mon Mar 16 2015 - 05:00:03 PDT
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