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

From: Gustavo Seabra <>
Date: Fri, 31 Aug 2007 13:41:18 -0400

Hi Francesco,

I believe there's a confusion here. SolvateCap and solvateBox are LEaP
commands, used to build the system, and sander knows nothing about
them. Whatever way you choose to build your system is fine for sander,
as long as you get a reasonable system in the end. The way the system
was created has absolutely nothing to do with being able to run QM/MM
or DFTB calculations on it.

You *can* perfectly create the system in any way you want it, using
solvateCap or solvateBox or something else and, as long as it is
relaxed [e.g. following your suggested steps (1) to (5)], you can run
QM/MM on it. Depending on your system behavior, you may be able to
skip step (6).

Now, if you want to use periodic boundary conditions (PBC), then you
need to have a rectangular box (*created* in LEaP using solvateBox).
This is not only for DFTB: All of the QM methods in Amber9 can use
only rectangular boxes. Amber10 will have support for truncated
octahedral boxes in QM/MM (*created* in LEaP using solvateOct).

Notice that the only difference between QM and MM methods here is the
fact that Amber9's QM needs the box to be rectangular. For *ANY* PBC
calculations, you DO NEED A BOX, rectangular or octahedral. Water caps
are *NOT* appropriate for PBC calculations, QM or otherwise.

The only difference between DFTB and the other QM methods in Amber9 is
the treatment of long-range electrostatics and implicit solvation. For
all other methods you can use Ewald/PME and GB, but not for DFTB.


On 8/30/07, Francesco Pietra <> wrote:
> 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 - 06:07:35 PDT
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