Re: [AMBER] A query on using a non-standard solvent

From: Steinbrecher, Thomas via AMBER <>
Date: Wed, 1 Feb 2023 10:11:57 +0100

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 ( 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,


On Wed, Feb 1, 2023 at 9:49 AM devendra.prajapat.cys19--- via AMBER <> 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
> _______________________________________________
> AMBER mailing list

*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
Phone +41 61 682 1319
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Received on Wed Feb 01 2023 - 01:30:03 PST
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