AMBER Archive (2006)

Subject: Re: AMBER: ab initio terminology query

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Wed Nov 01 2006 - 12:27:44 CST

Hi Ross,
standard notation is single point//geometry for few decades.
If it is written differently then it is a strange
terminology and is confusing.
I would suggest to correct it.

Best wishes, Jiri
.
>
> > > In the following example: Data was computed at the
> > > "B3LYP/6-31++G(2d,2p)//HF/6-31G(d) level of theory"
>
> > Lower level (HF in this case) is optimization,
> > higher level (DFT) is the single point property calculation.
>
> I disagree with this. The ethos of the Amber force fields is that a
> consistent model is used for the charge calculation and then the individual
> parameters are fitted with this charge set in mind. It is extremely
> important when calculating new RESP charges that the same level of theory be
> used for the charge calculation as was used in the rest of the force field.
>
> In the case of the FF94, 96, 99XX force fields the level of theory used for
> the single point calculations was HF/6-31G(d). The reason for this is that
> this combination fortuitously underestimates the charges in gas phase giving
> charges that are more consistent with being in solvent. Hence this
> systematic error is used obtain solvent phase resp charges from a gas phase
> simulation of a residue. The FF03 force field uses a different level of
> theory for the charge calculation that includes an implicit solvent model to
> obtain solvent phase charges. If you use a higher level of theory for the
> ESP calculation you will over polarise your molecule when simulating it in
> solvent.
>
> As such one should not change the level of theory used for the single point
> part of the calculation without a detailed understanding of why it was
> chosen to be that in the first place. With regards to the optimisation part
> of the calculation I think one could discuss this for ever. Francois can
> probably comment here but I think the generally accepted 'optimum' method is
> to do the calculation over several conformations and average the resulting
> charges. In all cases the single point ESP should be calculated using the
> same level of theory as the rest of the force field was fit to.
>
> So with regards to the above statement, if the authors are specifically
> referring to RESP charge derivation for an AMBER force field then they mean
> they used B3LYP for the optimisation and then HF for the ESP generation.
>
> However, with regards to QM calculations in general I have no idea what the
> general consensus is. Ideally I think people should explicitly state what
> they did rather than use a confusing and ambiguous notation.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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