Hi Lin
> For one molecule, will Amber give the same set of force field parameters
> to this molecule no matter this molecule is put in
> water or in vacuum?
> The bond length, the bond angle, and the dihedral angles of the same
> molecule will be different in water and in vacuum.
> So, will the force field parameters be changed/ adjusted in water than in
> vacuum?
The parameters will be the same regardless of whether it is in vacuum or
solvent. You have to bear in mind though that the act of having the solvent
there is what perturbs the bonds, angles etc. Hence if you were to refit
them all then you would be effectively including the solvent effect twice.
You should also be aware that the amber force field parameters are designed
for simulation in solvent. E.g. the RESP charges use HF/6-31G* which is
deliberate since it has a systematic error that means from a gas phase
simulation it gives effectively solvated charges. Thus one should appreciate
that this means that a vacuum simulation will not strictly be correct using
the current charges.
> How does Amber set the force field parameters for the molecule?
See Cornell et al. JACS, 1995, 117, p5179.
> I mean..... are the force field paramters determined in local or in
> global?
Local by atom type for bonds, angles, dihedrals etc. Charges are by
determined by residue. The entire thing is additive.
> Could I change parts of the force field parameters which I found from the
> published paper?
Yes - see the following tutorial for an example of building your own
residues: http://www.ambermd.org/tutorials/advanced/tutorial1_adv/index.htm
> Or, I could not change parts of the force field parameters; instead, I
> have to change the whole set of the force field
> parameters???
This is somewhat of a philosophical question ;-). You are fine to introduce
your own charges and parameters for individual amino acids retaining the
rest of the force field parameters for the other residues. The whole thing
is designed to work like this as building blocks off of a set of underlying
atom types and residues. There is of course the temptation to refit
everything globally for a given system but of course then you lose
transferability and you are falling into the trap of over fitting. So in
reality should everything be refit, should parameters / charges etc change
as a function of environment? Yes... Do you have infinite computer power?
No... In an ideal world we'd probably do everything as full QM CI
calculations but of course in reality approximations have to be made.
That is probably more information that you needed...
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sun May 25 2008 - 06:07:32 PDT
