Hi Hayden,
> "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."
>
> Confuses me...according to the gaff paper (Development and
> Testing of a
> General Amber Force Field. J Comput Chem 25: 1157-1174, 2004)
> the gaff bond
> parameters are calculated at (MP2/6-31G*), yet the charges
> are derived at
> HF/6-31G*. This is one example of a few in which the charges
> are obtained at
> different levels of theory to the other parameters.
Sorry, let me clarify what I meant by this statement. I was referring
'implicitly' to someone creating their own residue to be modelled as a
non-standard residue in a protein containing lots of standard amino-acids.
In this case what I meant was the method used to obtain the RESP charges for
the non-standard residue should really be consistent with the method that
was used to obtain the RESP charges for the standard amino acids. I wasn't
referring to any other parts of the force field fitting, bonds, angles etc.
I hope that makes sense.
With regards to the B3LYP/6-31G++(2d,2p)//HF/6-31G(d) statement on page 23
of the manual I think it is important to look at the whole sentence:
"All valence parameters were determined by fitting to data computed at
B3LYP/6-31G++(2d,2p)//HF/6-31G(d) level of theory."
The important point here is the word valence. In other words they are not
referring to the charge model used but instead to the bonds, angles etc. As
such this is not such a confusing statement. They used HF/6-31G* to do the
optimisations and then single point B3LYP on top of this. In this case the
notation is inline with what others have stated and makes perfect sense. It
was the issue of it being related to the calculation of the electrostatic
potential that made it possibly confusing.
I will leave the issue of what methods are used for RESP on what force
fields to the respective developers since they should be able to answer more
definitively.
All the best
Ross
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Hayden Eastwood
> Sent: Wednesday, November 01, 2006 12:13
> To: amber.scripps.edu
> Subject: RE: AMBER: ab initio terminology query
>
> Hi Guys
>
> Thanks for the feedback. The example question
>
> "Data was computed at the B3LYP/6-31++G(2d,2p)//HF/6-31G(d)
> level of theory"
>
> actually comes from the AMBER manual (sorry, should have
> mentioned this!),
> page 23 under the Glycam-04 force field section. Indeed, my own
> understanding of the problem has been that:
>
> 1. Optimisation should be carried out at whatever level of theory is
> computationally feasible (ie better optimized structure = better final
> partial charges).
>
> 2. ESP charges for solution phase residues should be derived at the
> HF/6-31G(d) level of theory for
> the reason that Ross stated (ie fortuitous cancellation of errors that
> permit the modelling of a solvent polarized environment).
>
> 3. ESP charges for gas-phase should be calculated at the
> B3LYP/cc-pVTZ level
> of theory because this level (being more accurrate than
> HF/6-31G*) doesn't
> exagerate the dipole moment and hence better represents a
> non-polarizing
> gas-phase environment.
>
> Please correct me if I'm wrong on this...
>
> At the risk of making this discussion laboured I have a few final
> clarifications to make:
>
> 1. I am developing some sugar residues (for use within an
> implicit solvent
> environment) using the gaff parameter set. Am I right in
> presuming that I
> should use HF/6-31G* to get the partial charges? I chose this
> charge model
> for the reason that Ross gave (fortuitous cancellation blah
> blah...) and
> because it's consistent with the charge model of the GLYCAM
> force field
> sugar residues. However, Ross's earlier comment:
>
> "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."
>
> Confuses me...according to the gaff paper (Development and
> Testing of a
> General Amber Force Field. J Comput Chem 25: 1157-1174, 2004)
> the gaff bond
> parameters are calculated at (MP2/6-31G*), yet the charges
> are derived at
> HF/6-31G*. This is one example of a few in which the charges
> are obtained at
> different levels of theory to the other parameters.
>
> Sorry, please bear with me on this, I'm trying to get to the
> bottom of the
> many (apparently) contradicting views on this issue that I've
> heard over the
> last 8 months....
>
> 2. Is it safe to assume that I can use the ff02.pol.r1 force field to
> perform explicit water calculations? Presumably it doesn't
> matter that the
> B3LYP/cc-pVTZ derived charges don't account for the average polarizing
> nature of the solvent because the ff02 parameter set
> introduces the required
> polarization arising from the explicit solvent.
>
> 3. If I wish to run the gaff parameterized sugar molecule in
> explicit water,
> do I need to change the charge model from HF/6-31G* to
> something else? If I
> believe Ross's statement from earlier:
>
> "The FF03 force field uses a different level of theory [to
> HF/6-31G*] 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."
>
> Again I'm confused here...according to the reference given on
> page 20 of the
> amber manual (the ff03 united atom force-field section):
>
> "...this force field [The united atom one] uses the same
> charging scheme as
> ff03...".
>
> When I looked up the reference for this, I saw that the
> charges were derived
> at the B3LYP/cc-pVTZ level, which is the same as that mentioned in the
> manual for the ff02 force field. If the ff02 force field
> describes gas-phase
> charges and the ff03 force field approximates solvent charges
> (each of which
> will be different in nature), then why do they have exactly
> the same basis
> set for deriving the charges?
>
> Please help me out here!
>
> Best
>
> Hayden Eastwood
>
>
>
>
>
>
>
>
>
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Received on Sun Nov 05 2006 - 06:07:15 PST
