Re: [AMBER] hydophobicity

From: Jason Swails <>
Date: Wed, 26 Nov 2014 18:28:04 -0500

On Tue, Nov 25, 2014 at 2:59 AM, Mary Varughese <>

> Sir,
> is there any way to quantify or qualify the hydrophobicity of
> nucleobases involved in stacking in amber.?

​There is no "hydrophobic"​

​ part of the potential energy function in any of the "typical" force
fields (e.g., Amber, CHARMM, GROMOS, ... etc.) -- it is a side-effect of
the nonbonded interactions (electrostatic and van der Waals). Quantifying
it would require an actual formula that defines it, and I'm not familiar
with any such formula.

As far as getting a qualitative measure -- it seems to me that
hydrophobicity would correlate (probably strongly?) with the solvent
exposed surface area of those residues, so I would probably use that
relationship in order to compare "hydrophobicities" of different residues.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 26 2014 - 15:30:02 PST
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