AMBER Archive (2008)


From: FyD (
Date: Wed Dec 17 2008 - 03:12:38 CST

Hi Ross,

> For example if you would be kind enough to re-write section 1 of the
> Tutorial A1

OK, we will work on that.
Give us a little time as we are in the process of releasing R.E.D. Server...

> It would be great to have a tutorial on the AMBER site that shows
> how 'modern' charge derivation should be done (at least in an
> introductory fashion) in a way that couples it in with building a
> system from scratch. It can then of course include links to more
> complex examples / considerations.

I 100 % agree.

The starting point would be a "classical" way, i.e. as it was done in
the building of the AMBER FF topo. DB (Cieplak et al. JCC, 1995) -
because (i) we are talking about "AMBER", & (ii) nobody did better so
far (also describing some limitations/problems encountered in this
work) & then in a second step provide directions to
modified/complexified approaches to solve those limitations/problems.

> Thinking longer term would it not make sense for R.E.D. to be
> included in AmberTools? Dave Case would have to comment here but it
> seems to me that at least in some form, even if it was just an empty
> directory with README's in etc it would make sense.

I have already discussed twice with Dr Case about this point.
We need more time here, and I do not have his huge experience.
Finally, as I said to Dr Dodson, AmberTools did not become GNU in one day.

I will contact you to your private email.

regards, Francois

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