Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system

From: Him Shweta <>
Date: Wed, 18 Mar 2015 15:39:10 +0530

Thank you so much for your reply sir.

On Tue, Mar 17, 2015 at 9:10 PM, Thomas Cheatham <> wrote:

> > I want to calculate the electrostatic interaction energy for a DNA-Ligand
> > system in explicit TIP3P water.
> > where, E=k·q1·q2/r and k (=1/4πε) and value of k = 332.24 for
> > converting the energy in Kcal/mol.
> > Here i want to know that dielectric constant that will be used for
> > dna-ligand in explicit TIP3P water system is (~60). So, am i right that
> the
> > final E=k·q1·q2/r*60 Kcal/mol for my system.
> As Jason points out, in explicit water you would want to set the
> dielectric constant to 1 since the effective dielectric screening is done
> by the explicit TIP3P waters, i.e. at short range there is no screening
> (since a water cannot fit between the close point charges); at longer
> range, bulk water will effectively screen by ~80 (i.e. you do not have to
> screen artificially by setting the dielectric constant is 80). If you did
> not have explicit water (i.e. you stripped it), you could apply a distance
> dependent screening (as was done in the old days) or even a more
> complicated sigmoidal screening, however this gets complicated with
> heteregenous systems (with differential screening), large solutes, etc.
> If a heterogeneous system, likely better is to use an implicit solvent
> like generalized Born (after stripping the water, as per MM-GBSA).
> Based on the discussion above, the "dielectric" constant for a atomic /
> molecular system is misleading since it is bulk property and is likely not
> constant at atomic/molecular scales.
> --tec3
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Received on Wed Mar 18 2015 - 03:30:03 PDT
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