Re: [AMBER] Organic solvent box - Amber do not see the molecule but its atoms

From: David A Case <>
Date: Tue, 24 May 2016 09:03:37 -0400

On Tue, May 24, 2016, Stregone wrote:
> I am doing a acetone box. I did find useful information in
> -
> -

Once you create an acetone UNIT (molecule), you can either use packmol
to create a box full of these (just save in pdb format), or you can
use solvateBox to build this.

> I realised that Amber only see the atoms, but not the molecule.

How did you arrive at this conclusion? To be of any help, we need to know
exactly what commands you used, and what you saw. How did you create the
acetone unit?

> I have been using the pdb and mol2 files from the the project in R.E.DD.B.

This is probably fine: we just don't know (from your description) what you did
in LEaP.


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Received on Tue May 24 2016 - 06:30:03 PDT
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