Re: About QM-MM

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Aug 29 2007 - 11:34:45 CDT

I don't know Gamess-US (I use NWChem). Are you talking of semiempirical or "ab
initio" QM? Of course, "ab initio" wouldn't be viable for molecules from medium
size (60 atoms) on.
francesco

--- Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:

> Hi
> If you can interface NAMD with some open source QM package like GAMESS-US
> then it will be good. then both NAMD and QM package will be open source.
> Dhiraj
>
> On 8/29/07, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> >
> > 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.
> >
> > francesco
> >
> > --- 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.
> > >
> > > 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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>
> --
> Dhiraj K. Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
>

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