Dear Yun,
> As in Glycam_06g.dat, the sulfane sulfur is defined as atom type "SM", which
> has some preliminary parameters for thiosugars.
You are right - my mistake.
> But no atomic charge was
> developed for this SM atom in any molecule within the prep file. Anyways, I
> have to validate these parameters.
Charges are never compute for an atom type; in general charge values
are not transferable between molecules. So you need to derive the
charge values for each new molecule.
> Could you go into some detail about "follow QM data obtained using high
> theory levels"?
See for instance Duan et al.
http://onlinelibrary.wiley.com/doi/10.1002/jcc.10349/abstract
> Because I thought since we are simulating molecules in
> condensed phase, i.e., in solution, it should be better to calibrate MM
> parameters with conformational behaviors in solution instead of "in vacuum".
Well, you are right. Many things to discuss here ;-) uff... In short,
- HF/6-31G* is used in MEP computation to induced implicit polarization.
- FF parameter determination is generally carried out in gas phase
(highly related to the FF model)
> And except plotting potential energy graph with respect to dihedral values,
> I am not sure how to validate angle parameters...
You fit MM to QM energies to get your FF parameters - very short
sentence for a complex problem ;-). Then, you validate in MD
simulations following whatever experimental/QM data you have: NOEs
i.e. distances, conformation populations, dihedral values in relation
with QM, the establishment of specific hydrogen-bonds, NMR 3J coupling
constants, what else? I guess many stuffs ;-)
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 22 2011 - 00:30:03 PDT
