From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Aug 29 2007 - 01:38:17 CDT
The problem is not open or closed source (you can have ONION in open source QM
suites, as I have it). ONION is quite a different affairs from QM-MM.
--- Eduardo Tejera <edutp00_at_yahoo.com> wrote:
> 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.
> 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
> 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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