AMBER Archive (2006)

Subject: Re: AMBER: ab initio terminology query

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 01 2006 - 14:42:23 CST

On Wed, Nov 01, 2006, Hayden Eastwood wrote:
>
> "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.

OK. Note that the beginning of the first full paragraph on that page says:
*charges* come from RESP at HF/6-31G(d) level. That is the standard procedure
used for most amber force fields (except for ff02 and ff03).

The sentence you cite says *valence parameters* come from
B3LYP/6-31++G(2d,2p)//HF/6-31G(d). This means energy terms related to bonds,
angles and torsions, not the charges. This again makes reasonable sense: one
could argue about MP2 vs. DFT here, but Woods et al. used big basis DFT
single point calculations, at a Hartree-fock optimized geometry. Again, this
paragraph has nothing to do with charges, and the authors are using standard
quantum chemistry notation.

>
> 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?

Yes.

> 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."

Not sure what Ross really meant here....It is quite common to use different
levels of theory for different parts of the force field.

>
> 2. Is it safe to assume that I can use the ff02.pol.r1 force field to
> perform explicit water calculations?

Yes.

>
> 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?

No.

Note that the charge models for ff94/ff99/gaff use RESP HF/6-31G* charges by
default. The procedures used for ff02 and ff03 are different from this (and
different from each other). These are all arbitrary choices, but ones made by
the people who developed the various models.

You seem jumping around a lot in your quotes about force field charges, so it's
hard to see exactly what is confusing you (although it is indeed a somewhat
convulated subject). Note that, even though they may use the same basis set,
other parts of the procedure for getting charges for ff02 are different than
for ff03: the ff02 procedure "knows" that it is preparing charges for a
polarizable force field, and the ff03 procedure "knows" that is is making
charges for a non-polarizable force field. See the original papers for details
here.

...hope this helps....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu