[AMBER] Parametrization of new amino acid in methanol solvent

From: Chetna Tyagi <cheta231.gmail.com>
Date: Fri, 19 Jan 2018 13:10:51 +0100

Dear all,

I study a fungal peptide with non-standard residues like AIB, and
D-isovaline etc. I parametrized them using R.E.D server and used for
simulations in explicit water and methanol solvents.

I was recently advised that I should carry out the parametrization and
charge calculation of these residues in methanol solvent for accuracy. Is
it possible using R.E.D server? Because I searched through and I could not
find any such information.

Has anyone attempted to do it before? Is there a way in Amber to add
various solvent effects during parameterization?

Any help would be much appreciated.

Best wishes
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Received on Fri Jan 19 2018 - 04:30:02 PST
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