AMBER Archive (2008)

Subject: Re: AMBER: Which CO2 potential?

From: Jones de Andrade (johannesrs_at_gmail.com)
Date: Wed Jul 23 2008 - 22:45:00 CDT

Thanks a lot Gustavo.

I though about this possibility, but for me it looks like making an AMBER
water potential to make simulations with water instead of... spc/e or tip3p.
I was thinking if there isn't in the literature any "commonly used" CO2
potential together with AMBER parameters of other molecules in the
simulation. ;) Is there such a reference flying around?

Thanks a lot,

Jones

On Thu, Jul 24, 2008 at 12:32 AM, <gustavo.seabra_at_gmail.com> wrote:

> Hi,
>
> AFAIK, Amber doesn't have parameters for CO2. I believe that, in your
> situation, your best bet is to generate the parameters yourself. You
> can use Antechamber to generate GAFF parameters for it. Take a look
> at:
> www.ambermd.org/tutorials/basic/tutorial4/index.htm
> For details on using Antechamber.
>
> HTH,
> Gustavo.
>
> On 7/23/08, Jones de Andrade <johannesrs_at_gmail.com> wrote:
> > Hi all.
> >
> > I have a really direct question: I have to make a few simulations
> involving
> > interation of CO2 molecules with other, with the other molecules,
> solvents,
> > etc, all within the AMBER ff.
> >
> > Which potential should I choose to describe the CO2 molecule? Any
> > suggestion, please?
> >
> > Thanks a lot in advance,
> >
> > Jones
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