Subject: RE: minimization of a crystal structure

From: AM <[email-masked]>
Date: Tue, 14 Mar 2000 13:54:00 -0500 (EST)

Dear Jonathan,
 If you optimize starting form experimental structure, almost any force
field will work. Even solid spheres. If you search for the lowest among
many local minima, it's another story. For an example, see the recent
paper from Sheraga's group (JACS, 2000, 122, p.907). They found AMBER FF
to work a little better then DREIDING.
 I see no reason to introduce dielectric constant in description 
where all molecules are treated explicitly (like crystal). If you have any
arguments in favor of it, I'd be happy to learn.
 Use of the distance-dependent dielectric constant may be appropriate to
describe two solute molecules if the solvent between them is more
structured, than in the bulk (like water). But there is no disordered 
water in crystals of small molecules!

Regards,
Artem Masunov

Jonathan Baell <[email-masked]> wrote:

> Does anyone one have any references on the use of MMF94 ( with modified
> amide parameters for static minimizations, a la MMF94s as implemented in
> sybyl 6.5) for minimization of a crystal structure of a small molecule
> such as, for example, a substituted benzanilide?
> This is especially in regard to choice of dielectric function (e.g.
> distance-dependent with base diel. of 4?) to best approximate the
> solid-state electrostatic environment.

The latest review on crystal structure minimization can be found in the
long introduction to the paper from