AMBER Archive (2008)

Subject: Re: AMBER: /dat/slko

From: Gustavo Seabra (
Date: Thu May 22 2008 - 12:00:36 CDT

Hi Francesco,

> I had downloaded the new files of data. Do you know if improved?

As Ross said, no. The parameters are exactly the same. The changes in
the files are just the naming conventions, and the additional xml
section in the end with a description of how parameters were obtained.
(This xml session is just ignored in the calculations.)

> 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, [...]

That alone provides a hint that DFTB would probably not work well. If
you look in the xml part of the new files, you'll notice that all of
them used B3LYP/6-31G* in the calculation of the repulsive potentials.

> 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"

So, did M05-2X work fine? If so, you it may be interesting for you to
take a look at the new Amber/PUPIL/Gaussian interface available in
Amber10. Take a look at:


Where this interface is discussed.

> 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.

Yes, that should cover most applications. However, Amber10 does not
limit the possible atoms anymore, so you can use whatever atoms you
want, as long as you have the needed slko files. That allows you to
download any parameter set form and use it with Amber10. Just
make use that, if you need to use files from different sets, the sets
are compatible.

> I take also the opportunity to ask if Amber9 can be removed or if it
> might be useful alongside Amber10 (neglecting comparisons, of course).

There have been some changes in output format from Amber9 to Amber10.
Right now REMD comes to mind. So, you *may* want to keep Amber9 around
just until the users get comfortable with the new formats. (But that's
just *my personal* opinion.)

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