Thanks to Petr, Jiri, and Ilyas for your comments. After rereading your papers, I have a little more insight...
Figure 6 in the Zgarbova paper was the critical one. The FF99 chi DIHEDRAL TERM is exactly what I was asking about. I can now see how it might have been rationalized to 'push' chi off a pure anti (chi = 180 degrees) form, and how this, in concert with all the other parameters, might lead to chi minima at approx. 60 and 200 degrees.
I just though a Vn/2 of 2.5 kcal/mol, leading to a 5 kcal penalty, was pretty dang high. It's clearly a little more complicated.
Steve
-----Original Message-----
From: Petr Jurecka [mailto:jureckap.gmail.com]
Sent: Friday, August 09, 2013 10:20 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Chi torsions
Dear Steven,
it appears that the V1 term of chi in ff99 is not physically motivated. In Cornell et al., JACS 1995 on page 5187 I found the following explanation for V1 (and V2, which has been removed in ff98):
"We thus constructed a simple test case where adenine is attached to CH-(OH)-CH3, with the dihedrals constrained to mimic the C2' endo conformation of a sugar ring (Figure 1) and carried out MP2/6-31G*//HF/6-3
lG* ab initio calculations as a function of x with this model. As one can see from Table 10, with no additional dihedral parameters, the energy difference between the syn and anti minima is significantly overestimated with our initial model. We thus chose to add explicit dihedrals (V1 and V2) (see Table 14) around the glycosidic bond to bring the two minima into qualitative agreement."
It seems that V1 was added empirically to match the relative syn/anti energies calculated by MP2/6-31G*//HF/6-3 lG*
Best regards
Petr
On Fri, Aug 9, 2013 at 11:06 AM, Jiri Sponer <sponer.ncbr.muni.cz> wrote:
> Dear Steven,
>
> I think you need to distinguish between just single a dihedral term,
> sum of dihedral terms, full torsion energy profile, then even full
> energy profile with inclusion of solvent effects and finally torsion
> simulation behavior which even includes balance between the water
> model and the solute ff.
> The final force field performance
> is the key issue (the target) and it often may differ from what you
> try to guess from some single energy terms.
>
> cf. figs. 2-6 in
> Refinement of the Cornell et al. Nucleic Acids Force Field Based on
> Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
> Zgarbova et al.
> JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 7 Issue: 9
> Pages: 2886-2902 SEP 2011
>
> Fig. 2 in:
> Reference Simulations of Noncanonical Nucleic Acids with Different chi
> Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and
> Z-DNA Krepl et al. JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume:
> 8
> Issue: 7 Pages: 2506-2520 JUL 2012
>
> Another issue is the (un)physical meaning of the torsional term, which
> effectively is used to tune the final performance of the force field,
> i.e., it depends on the other parameters.
> The DNA and RNA sugar-phosphate backbone emerges as the key player. An
> overview of quantum-chemical, structural biology and simulation studies
> Sponer et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 14 Issue: 44
> Pages: 15257-15277 2012
>
> A Novel Approach for Deriving Force Field Torsion Angle Parameters
> Accounting for Conformation-Dependent Solvation Effects Zgarbova et
> al.
> JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 8 Issue: 9
> Pages: 3232-3242 2012
>
> Best wishes, Jiri
> -------------------------------------------------------
> Jiri Sponer
> Institute of Biophysics
> Academy of Sciences of the Czech Republic Kralovopolska 135
> CZ-61265 Brno
> Czech Republic
> e-mail: sponer.ncbr.ncbr.muni.cz
> fax: 420 5412 12179
> phone: 420 5415 17133
> http://www.ibp.cz/
> http://www.ibp.cz/en/departments/structure-and-dynamics-of-nucleic-aci
> ds/
> -----------------------------------------------------------
>
>
>
> On Thu, 8 Aug 2013, Steven M. Graham wrote:
>
> > Date: Thu, 8 Aug 2013 16:57:43 -0400
> > From: Steven M. Graham <grahams.stjohns.edu>
> > Reply-To: AMBER Mailing List <amber.ambermd.org>
> > To: "amber.ambermd.org" <amber.ambermd.org>
> > Subject: [AMBER] Chi torsions
> >
> > I'm sure I could find on my own (eventually), but can someone
> > explain
> the rationale for the FF99 chi torsion parameters? (Vn/2 = 2.5
> kcal/mol, 1-fold, 0 degree phase shift; chi is OS-CT-N*-CK. CK is a
> purine C8.) Because that function predicts a minimum energy when the
> OS-CT-N*-CK angle is 180 degrees, which is the syn conformation.
> >
> > Steven M. Graham, Ph.D.
> > Associate Professor
> > Department of Chemistry
> > St. John's University
> > 8000 Utopia Parkway
> > Queens, NY 11439
> >
> > grahams.stjohns.edu
> > Office: 335 St. Albert Hall
> > Voice: 718-990-5217
> > Fax: 718-990-1876
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Fri Aug 09 2013 - 13:00:03 PDT
