AMBER Archive (2006)

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

From: Eric Hu (list.eric_at_gmail.com)
Date: Wed Aug 09 2006 - 16:30:04 CDT

Thanks, Dr. Case. This has solved my problem.

Regards,
-Eric

On 8/9/06, David A. Case <case_at_scripps.edu> wrote:
> 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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