Re: About QM-MM

From: Eduardo Tejera (edutp00_at_yahoo.com)
Date: Tue Aug 28 2007 - 18:26:48 CDT

These are great news without any questions.
   
  I think that is very intersting the problem of interaction between small molecules and proteins were the QM-MM can be applied as a very usefull tool. We can use ONION in Gaussian with good results in several case but this software is not open source like NAMD and with the posibility of "scripts" the spectrum of applications is very wide. I think that the use of semiempirical methods as well as DFT could be available.
   
  Best
  Eduardo

Francesco Pietra <chiendarret_at_yahoo.com> escribió:
  Hi Chris:
These are wonderful news.

Of my interest is the interaction of the "organic molecule" (read: natural
products, drugs) with biopolymers. Even the first simple step of studying the
conformations of the "organic molecule" under the influence of the environment
could be best approached by QM-MM.

I foresee two problems:
(1) Semiempiricals like MNDO, PM3, AM1 deal very poorly with conformational
problems. Perhaps, DFTB is better to this respect.
(2) Parameters for the "organic molecules". However, Jan Saam just a few days
ago has promised to develop Paratool, once is PhD examinations are over.
Paratool could solve these problems, provided it is made simple (automatic)
enough to become manageable by the organic chemist.

Best wishes

francesco pietra

--- Christopher Harrison wrote:

> Hi Francesco,
>
> We are currently in the early stages of planning and developing a QM-
> MM implementation for NAMD. There's obvious interest from the
> community as well as our own group for this functionality.
>
> We'd be happy to hear about any specific types of QM-MM calculations,
> functionalities or applications that might be useful to those
> interested.
>
> Best,
> Chris
>
> Christopher Harrison
> Postdoctoral Research Associate
> Theoretical and Computational Biophysics Group
> University of Illinois at Urbana-Champaign
> char_at_ks.uiuc.edu
>
>
> On Aug 28, 2007, at 8:18 AM, Francesco Pietra wrote:
>
> > I wonder why no QM-MM in NAMD. Is that because of disbelief in
> > semiempirical
> > electronic calculations, such as MNDO AM1 PM3 DFTB, or is just
> > because no
> > developer has yet had time to consider that facet?
> >
> > The other side of the coin is MD included in well established QM
> > code suites,
> > which become unmanageable with molecules of common interest.
> >
> > These are not intended to be provocative questions. To the
> > contrary, views
> > about QM-MM from the two sides may help planning research in the
> > scientific
> > community.
> >
> > Thanks
> >
> > francesco pietra
> >
>
>

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