AMBER Archive (2009)

Subject: Re: [AMBER] Any link to a major QM code?

From: Francesco Pietra (
Date: Mon Feb 16 2009 - 08:47:04 CST

I sincerely apologize for my md-mm. Also, I forgot about PUPIL, which
I heard about some time ago.

While interfacing with Gaussian is of little interest for me, hearing
about interfacing with nwchem and gamess is of great interest. Why not
mpqc? It is fast. It was born parallelized. It is GNU. It is written
in C. It is object oriented. No recent density functional and no
excited states but supporting it by linking amber to it might break
the ice.

Thanks indeed and again very sorry for my typo.


On Mon, Feb 16, 2009 at 3:59 AM, Adrian Roitberg <> wrote:
> To expand on Gustavo's answer.
> Amber has been interfaced with Pupil, a 'broker' program.
> So far it talks to gaussian and siesta on one side, and amber (and dlpoly)
> on the other side.
> See:
> "A versatile AMBER-Gaussian QM/MM interface through PUPIL." Juan Torras,
> Gustavo de M. Seabra, Erik Deumens, S.B. Trickey and Adrian E. Roitberg.
> Journal of Computational Chemistry. 29:10, 1564-1573 (2008)
> for the general ideas, and:
> "A Multiscale Treatment of Angeli's Salt Decomposition"
> Juan Torras, Gustavo de M. Seabra and Adrian E. Roitberg
> J. Chem. Theory Comput., 2009, 5 (1), pp 37–46
> For a particular application.
> We are working on adding the following implementations at this time:
> gamess
> nwchem
> Q-chem
> The API for Pupil should allow almost anyone to add whatever program you
> desire. In fact, we would love some help with a couple of the
> implementations.
> Cheers
> Adrian
> Gustavo Seabra wrote:
>> On Sun, Feb 15, 2009 at 12:58 PM, Francesco Pietra wrote:
>>> I came across an internet unofficial announcement of charmm software
>>> having been linked to gamess-us software for executing md-mm. If true,
>>> i guess it was a move from the charmm side as gamess-us is free
>>> software (which i am installing for resp charges).
>> What do you mean by md-mm? If what you are looking for is just being
>> able to do QM/MM MD, where the QM part is calculated by an external QM
>> program, we've had this in Amber for a while now, through the PUPIL
>> interface.
>>> Question: is any similar plan from the amber side? I suspect that dftb
>>> will not be enough, as far as md-mm is concerned, although all that
>>> glitters may not always be gold.
>> I don't really understand what you mean about DFTB here... It is not
>> an interface with an external program: The DFTB implementation is all
>> inside Amber, just as any other QM method available there.
>> Gustavo.
>> _______________________________________________
>> AMBER mailing list
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email
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