AMBER Archive (2008)

Subject: RE: AMBER: /dat/slko

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 22 2008 - 10:24:47 CDT

Hi Francesco,

The parameters from dftb.org for amber 10 are the same as those for amber 9. The only difference is the file naming. It is possible that newer parameter sets could be developed to improve DFTB but I don't think there are any at the moment. Have you tried turning on dispersion to see if that helps?

Also AMBER 10 supports PME and GB for DFTB so this may help you but I suspect not.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Francesco Pietra
> Sent: Thursday, May 22, 2008 2:15 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: $AMBERHOME/dat/slko
>
>
> Hi:
> please see spl/skf below
>
>
> --- On Wed, 5/21/08, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
>
> > From: Gustavo Seabra <gustavo.seabra_at_gmail.com>
> > Subject: Re: AMBER: $AMBERHOME/dat/slko
> > To: amber_at_scripps.edu
> > Date: Wednesday, May 21, 2008, 7:29 AM
> > On Wed, May 21, 2008 at 8:47 AM, Francesco Pietra
> > <chiendarret_at_yahoo.com> wrote:
> > > I do not remember as I filled in the parameters for
> > dftb in Amber9.
> > >
> > > Now, installed Amber10 (with only problems as to QMMM,
> > which are being clarified), I wonder whether the directory
> > >
> > > $AMBERHOME/dat/slko
> > >
> > > has to be created. In the current installation
> > $AMBERHOME/dat/ does not comprise slko.
> >
> > It should have been created by the installation, since some
> > files
> > (other than the SK parameters) are distributed with
> > Amber10. However,
> > if the directory is not there, you should create it.
> >
> > Notice that two files (DFTB DISPERSION.INP_ONCHSP and
> > CM3_PARAMETERS.DAT) were accidentally left out of the
> > installation, so
> > you'll need to download those from the Amber webpage if
> > you want to
> > run DFTB with dispersion or calculate CM3 charges.
> >
> > Note also that the naming convention for the SK files has
> > changed
> > before Amber10 release. They are now as [Atom1]-[Atm2].skf
> > instead as
> > [atom1][atom2].spl as they were before. So, to use the old
> > files in
> > Amber10 you'll need to rename them. For example,
> > "co.spl" should be
> > renamed to "C-O.skf" and put into that directory.
> >
> > Gustavo.
>
> I had downloaded the new files of data. Do you know if improved? With the
> old parameters and Amber9 I could do little for highly conjugated
> compounds: the dftb minimized conformations were far from reality, much
> like with PM3 and the other semiempiricals. Actually, even B3LYP proved
> inadequate, so that I had to stick to vacuum (as COSMO and the others also
> proved inadequate for the tiny differences in conformational energies): F.
> Pietra “Why colchicine does not show mutarotation. With M05‑2X density
> functional in the realm of tricky natural products. J. Phys. Org. Chem.
> 2007, 20, 1102‑1107"
>
> At any event, if I understand, the only file for typical use in Amber10 is
> is the SCC file mio.0-1-tar.gz (S-O-N-C-H), the one I have used for slko.
>
> I take also the opportunity to ask if Amber9 can be removed or if it might
> be useful alongside Amber10 (neglecting comparisons, of course).
>
> Thanks
> francesco
>
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