Hi Devendra,
I would start by creating Amber parameters for Trehalose, or rather, since
it is just a sugar, check if glycam parameters for this molecule exist. To
build a system containing your protein in a trehalose solution, look into
packmol (
https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21224) to
assemble a starting conformation for your system. However, before even
looking at the protein simulation, I'd recommend running some simulations
of trehalose in water at various concentrations, to get a feeling for how
the mixture behaves.
Kind Regards,
Thomas
On Wed, Feb 1, 2023 at 9:49 AM devendra.prajapat.cys19--- via AMBER <
amber.ambermd.org> wrote:
> Dear Amber users,
>
> I want to study a protein in a specific concentration of trehalose
> solvent. Since this solvent is not available in default solvent
> libraries.
> Could anyone help me with how I can use trehalose pdb as a solvent?
>
> Many thanks in advance.
> Sincerely,
> Devendra
>
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--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Wed Feb 01 2023 - 01:30:03 PST
