From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Wed Aug 29 2007 - 11:31:00 CDT
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------=_Part_1324_33225001.1188405060991--
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