Re: [AMBER] Parametrization: consistency with gaff force field

From: Alechania Misturini <>
Date: Tue, 15 May 2018 08:55:07 -0300

Thanks David!

2018-05-14 11:25 GMT-03:00 David A Case <>:

> On Tue, May 08, 2018, Alechania Misturini wrote:
> > a question has arisen about the
> > consistency of generated parameters with the force field employed (GAFF,
> in
> > my case).
> You raise difficult questions, for which there are often no clear
> answers. One rule seems clear to me: if you want charges that are
> consistent with GAFF (and with GAFF2 and Amber force fields like ff14SB
> and our nucleic acid force fields,) you should use RESP charges with
> the HF/6-31G* basis. [AM1/BCC should be viewed as a fast but imperfect
> approximation to RESP/HF/6-31G*, to be used in cases where convienence
> and speed are more important than strict "consistency".]
> For energies, basis sets and methods have tended to improve as
> computers and codes have become faster. Here I personally see less
> reason to worry about "consistency" and more reason to be concerned with
> accuracy.
> > *Due the silicon atom present in the fragment, I need at least a triple
> > zeta basis set to better describe it, so, I did a benchmark with some
> > functionals and basis set (MP2, B3LYP and PBE0, with 6-31G*, 6-311G*,
> > def2-TZVP and cc-pVTZ). Fortunately I could find a similar x ray
> structure
> > to help me validate these results, and pick the best level of theory for
> my
> > case.*
> The above sounds OK to me: if one needs bigger basis sets for heavier
> atoms, that's what is needed.
> > *The same doubt rise about the structures used to parametrize with
> paramfit
> > or mdgx. Different QM level of theory than the employed in GAFF force
> field
> > can result in inconsistent parameters, looking the whole picture? (cause
> > just bonded parameters will be parametrized, LJ values will come from
> > and parm99 data, for Si)*
> Whether one should transfer Lennard-Jones parameters from GAFF/GAFF2 to
> new systems, or try to reparameterize them, it one of the difficult
> questions. Consistency would argue in favor of the former. If you are
> going to try to be consistent, I'd recommend using GAFF2 (not GAFF 1.x)
> as your "standard".
> Others may well have different opinions. Remember that GAFF(2) is
> indended to provide initial estimates of force fields that are often
> "good enough" for purposes like docking. If you have the time and
> knowledge to tweak the GAFF estimates for individual systems, you may
> well get better results.
> ...good luck....dac
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Alechania Misturini
Mestranda em Físico-Química
Bacharel e Licenciada em Química
Grupo de Estrutura Eletrônica Molecular –〈
*Departamento de Química – CFM*
*Universidade Federal de Santa Catarina – UFSC*
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Received on Tue May 15 2018 - 05:00:03 PDT
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