[AMBER] Ambertools coulomb constant

From: Gard Nelson <Gard.Nelson.NantBio.com>
Date: Tue, 2 May 2017 23:55:28 +0000

Hey Amber Gurus,

The other day, I came across a paper comparing the results of several simulation packages. (http://link.springer.com/article/10.1007/s10822-016-9977-1) They found that the electrostatic energy in AMBER disagrees with other simulation packages and suggest that the Coulomb constant in AmberTools may be outdated. The value used in AmberTools is slightly smaller (~10ppm) than the more current value, which should slightly decrease the electrostatic energy.

How big of an effect do you think this could have? If you figure the constant is low by 1 part in 10^5, that corresponds to reducing the charge on each atom by ~0.3%. That isn’t huge, but given that the electrostatic energy is extrinsic, I could imagine it having an effect.

Of course all of this should be irrelevant if the amber force fields were parameterized taking that value of the constant into account, right? What about the charges for small molecules that come from antechamber? Does antechamber have this value hard coded into it because I suspect that neither AM1-BCC or HF/6-31G* account for it. If charges from both the force field and antechamber are calculated assuming that Coulomb constant, then everything should be OK in Amber, but slightly off in other packages, right?

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Received on Tue May 02 2017 - 17:00:02 PDT
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