AMBER Archive (2007)

Subject: Re: AMBER: Tutorial protein-small-molecule-associates

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Fri Sep 14 2007 - 10:50:09 CDT

Hi,

On Tue, 11 Sep 2007, Francesco Pietra wrote:

> Is any tutorial available as to build a complex between a protein and a small
> molecule? Such, as for example, steptavidin-biotin, where the tutorial starts
> from the complex.
>
> Specifically I am interested in joining gaff (from antechamber) to ff99SB.

I do not know of such an Amber tutorial.
See this for suggestions:
http://amber.ch.ic.ac.uk/archive/200708/0300.html
See also this thread for a continuation of these issues:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-September/001178.html

Scott

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