AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10

From: Francesco Pietra <>
Date: Thu, 30 Aug 2007 06:17:41 -0700 (PDT)

With a 98-atoms non polymeric molecule, I just completed with Amber9 300ps of
constant pressure (1.0) MD in solvateBox of methanol according to (1)-(5)
below. This means that advice to carry out successful classical MD at const
pressure before const pressure QM-MM was excellent advice. However, the results
are such that the question below poses now differently.

AM1 distorts unacceptably the palatable conformation he received from classical
MD. I know by experience (in vacuum) that with multifunctional molecules, like
the present one, both MNDO and all forms of PM3 (including the one by
Jorgensen) are also unable to treat conformations.

I am left to the following alternatives:

(1) Extract potential energy for the solute from classical MD at constant
pressure. Is that feasible?

(2) Carry out (1)-(5) below, followed by (7), all that in solventCap (unless
the rst file from (5) below can be used to pass to solventCap, and hence (7)).

Thanks for your opinion

francesco pietra

--- Francesco Pietra <> wrote:

> Date: Wed, 29 Aug 2007 23:30:10 -0700 (PDT)
> From: Francesco Pietra <>
> Subject: Schedule for QM-MM with Amber9/Amber10
> To: Amber <>
> A guidance about the sequence of procedures for QM-MM with Amber9 in the
> perspective of Amber10 would greatly help planning at short or medium term.
> If - as published - DFTB performs better than other semiempiricals for
> conformational problems, should the sequence:
> (1) Minimization of solvent alone at const volume, 0K.
> (2) Minimization of the whole system at const volume, 0K.
> (3) Bringing the whole system slowly to 300K at const volume.
> (5) Equilibrating pressure at atmospheric value and md production.
> (6) QM-MM AM1 (or MNDO, or PM3 and variants)
> (7) QM-MM DFTB
> start with solvateCap? Or is any way to carry out (1)-(6) with solvateBox (as
> I
> am doing now) and use the results to perform (7) with solvateCap?
> If that change of solvation can not be performed, is any time schedule for
> Amber10 to become available? If I understand, (1)-(7) could be performed with
> solvateBox with Amber10. If so, it might become profitable to wait to carry
> out
> stage (7) until Amber10 becomes available. All that under the presumption
> (unchecked from my side) that solvateBox is more efficient than solvateCap.
> Thanks
> francesco pietra
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Received on Sun Sep 02 2007 - 06:07:18 PDT
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