AMBER Archive (2006)

Subject: Re: AMBER: cAMP ligand charge

From: David A. Case (case_at_scripps.edu)
Date: Mon Sep 11 2006 - 10:35:53 CDT

On Mon, Sep 11, 2006, Fenghui Fan wrote:
>
> Here is the commands to get the ligand charge:

The antechamber suite requires the net charge as *input*, that is, you have to
determine it by hand, by looking at the Lewis structure of the molecule for
example.

> If the GAUSSION is needed for this, where
> should we download it? I donot think AMBER has
> GAUSSION as its component.

You may be trying to run before learning to walk here. Try to get as much
out of the following tutorial as possible:

   http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/

Note that this is listed as an "intermediate" tutorial -- you will need to
have a basic understanding of using Amber from the more elementary work as
well. It is important not to just look for cookbook "recipes" that can be
typed in, but for procedures that you can understand.

...dac

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