AMBER Archive (2007)

Subject: AMBER: Solvent models

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu May 31 2007 - 10:23:56 CDT

As to solvents, the manual informs that besides
several polarizable models for water, non-polarizable
models are available for:

Chloroform
Methanol
N-Methylacetamide

What about the limitations of "non-polarizable" for MD
simulations with large, non-peptidic, non-nucleic,
non-polimeric (i.e. large natural products)?

In that context, are models for other solvents
available?

Just not to be too cryptic, I observed dramatic
solvent effects on CD spectra of such natural products
that imply conformational changes. The phenomenon
extends far outside the range of the above available
solvent models. I hope to get clues from MD
simulations.

Thanks

francesco pietra

       
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