Dear Karl,
> I have one small correction to point out. Much of Glycam06's
> energetic parametrization on neutral molecules was done using
> B3LYP/6-31++G(2d,2p) single-point calculations, performed on
> HF/6-31G(d) optimized geometries - not B3LYP/6-31++G**. This use of
> this theory and larger basis set comes from N.L. Allinger's study of
> carbohydrate energies (Lii et al J. Comput. Chem, 1999, 20, 1593),
> and is pointed out in the 2007 Glycam06 paper. The use of the basis
> set is important, since hybrid DFT results are very dependent upon
> the basis used.
ok thanks a lot for the update...
Concerning charge derivation (& NOT energy values):
Geometry optimization is carried out using HF/6-31G(d)... as in Cieplak et al.
See
http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
-1- RESP-A1A
HF/6-31G*//HF/6-31G* - Connolly surface algo. used in MEP computation
- 2 stage RESP fit qwt=0.0005/0.001
Used in the Cornell et al., Kollman et al., Cheatham et al., Wang et
al. & Hornak et al. AMBER force fields
-5- RESP-C2
HF/6-31G*//HF/6-31G* - CHELPG algo. used in MEP computation - 1 stage
RESP fit qwt=0.01
Used in the GLYCAM force fields
With R.E.D. Server (and R.E.D.-III.x & IV), we would like to propose
the exact theory level used by the authors of a published method
(HF/6-31G* for Cieplak et al., HF/6-31G** for Duan et al., and so...
HF/6-31G* for Kirschner et al.; i.e. what we currently propose - it
makes sense) by default i.e. when using R.E.D. III.x/IV & its mode 1
(
http://q4md-forcefieldtools.org/REDS/popup/popredmodes.php).
Then, any user - if she/he does not like the original approach - can
increase the theory level used in geometry optimization when using the
R.E.D. III.x/IV mode 2; i.e. by providing her/his own geometry
optimization output obtained with her/his own basis set choice...
regards, Francois
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Received on Fri Sep 23 2011 - 05:30:02 PDT
