AMBER Archive (2006)

Subject: Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 09 2006 - 15:45:42 CDT

On Wed, Aug 09, 2006, Eric Hu wrote:
>
> I am trying to use amber 9 to simulate a organic molecule in
> acetonitrile. Since ntb requires the box info in the topology file, I
> wonder if there is a way to treat acetonitrile as a solvent and use
> solvatebox command to add in the topology file in leap. Thanks.

Yes: use the solvateBox command in LEaP. If SOL is your solute unit,
and ACN is your acetonitrile unit, you should be able to say something
like this:

solvateBox SOL ACN 12.0

This should give you a box of acetonitrile moleucles around your solute.
It won't be very well equilibrated, so you will have to be make sure you do
that yourself, but this will get you started.

...dac

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