AMBER Archive (2008)

Subject: RE: AMBER: /dat/slko

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu May 22 2008 - 10:44:10 CDT

Hi Ross:
I am still at the organization level as far as QMMM is concerned. I am now accumulating ps for the pore protein-ligands of my studies. Not yet checked how dispersion can be turned on.
]
As to my disappointments with dftb with Amber9, must say that the colchicinoids proved very difficult to treat, requiring Zaho&Truhlar most recent functionals. The ligands of present study - with no conjugation between bonds - might well be amenable by Amber10-dftb. I'll try aside classical MD.

Thanks
francesco

--- On Thu, 5/22/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: AMBER: $AMBERHOME/dat/slko
> To: amber_at_scripps.edu
> Date: Thursday, May 22, 2008, 8:24 AM
> 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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> >
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