AMBER Archive (2006)

Subject: Re: AMBER: protein ligand complex

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Wed Feb 01 2006 - 11:53:06 CST

I would suggest working through the tutorials on the Amber
web site. Particularly useful may be the "protein with a nonstandard
residue" and "simulating a pharmaceutical compound". Then read
papers that use Amber to do the kind of thing that you want and
check their methods section carefully.

snoze pa wrote:

> Hi, I am a new user in amber community. I want to simulate my protein
> which has a ligand bound to it. This is a small
> organic molecule bound to the active site in the protein. I want to
> know how can i start my setup using this ligand and protein.
> Any help from scratch will be higly appreciated.
> thanks in advance.
> snoze

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