AMBER Archive (2008)

Subject: Re: AMBER: /dat/slko

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu May 22 2008 - 04:14:55 CDT

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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