AMBER Archive (2007)

Subject: Re: AMBER: organic solvent : hexan octan

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Wed Jan 24 2007 - 13:37:12 CST

Hi Sophie,

here is the link to the suggestion by Prof. Case at TSRI.

http://amber.ch.ic.ac.uk/archive/200611/0012.html

I am glad that Gustavo corrected me.

thanks,

jenk.

Sophie Barbe <sbarbe_at_insa-toulouse.fr> wrote: Thank you for your suggestion.
sophie

Selon Cenk Andac :

> 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 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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Chercheur Post-doctoral
Institut National des Sciences Appliquées
Groupe Ingénierie Enzymatique Moléculaire
Laboratoire Biotechnologie-Bioprocédés (UMR CNRS 5504/ INRA 792)
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