Re: [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA

From: Thomas Cheatham <>
Date: Fri, 27 Oct 2017 16:20:03 -0600 (Mountain Daylight Time)

> However, the publication by Miller et al., 2012, mentions that
> “the implicit solvent models utilized by are not parametrized
> to account for these species. Therefore, it is not recommended to
> include water or ions during the calculations”.

I think a better statement is that the implicit solvent models are not
*accurately* parameterized to account for ions. When we have included
specific ions in such calculations, we have altered the implicit solvent
radii to match solvation free energies and this has worked well. We have
also included explicit water at times.


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Received on Fri Oct 27 2017 - 15:30:02 PDT
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