AMBER Archive (2007)

Subject: Re: AMBER: organic solvent : hexan octan

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Jan 24 2007 - 13:12:40 CST

Sophie,

Before you try that, take a look at the amber-reflector archives. If
I'm not mistaken, there has been a recent discussioin here about the
use of GB with solvents other than water.

Gustavo.

On 1/24/07, Sophie Barbe <sbarbe_at_insa-toulouse.fr> wrote:
> Thank you for your suggestion.
> sophie
>
> Selon Cenk Andac <cenk_andac_at_yahoo.com>:
>
> > I do not have a library for hexane/octane solvent box. but I was just
> > thinking may be you could try a GB implicit solvent simulation and set its
> > dielectric constant to the solvent you want. For instance dielectric constant
> > for hexane is about 1.9 i believe...
> >
> > good luck..
> >
> >
> > jenk
> >
> > Sophie Barbe <sbarbe_at_insa-toulouse.fr> wrote:
> >
> > Hi amber users,
> >
> > I would like to perform a molecular dynamic of a protein in explicit organic
> > solvent: hexan or octan.
> > Do you have .lib files for these solvents? could you send them to me ?
> > Or otherwise could you explain me how can I generate these files?
> >
> > Thank you very much
> >
> > Sophie
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