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-acids/
-----------------------------------------------------------
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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Received on Fri Aug 09 2013 - 02:30:02 PDT
