ADL: Ligand atom types

Garrett M. Morris garrett at scripps.edu
Thu Mar 13 10:43:06 PDT 2008


On 10 Mar, 2008, at 2:23 am, Giulia Canevari wrote:

> Hi all,
>
> I can't find on the web site the list of ligand atom types that  
> Autodock 4
> can deal with.
>
> Could somebody direct me there (or tell me them), please?

The atom types and their parameters are listed in the parameter file,  
which in AutoDock 4.0.1 is called "AD4_parameters.dat".  You can read  
more here:

	http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters
	http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4


When AutoGrid and AutoDock 4 are compiled from source code into the  
executable, these parameters are "baked in" as the default values, so  
normally you don't need a copy of the AD4_parameters.dat file and you  
don't have to specify it explicitly in your GPF or DPF.

You can download the parameter file for AutoGrid 4.0.0 and AutoDock  
4.0.1 from here:

	http://autodock.scripps.edu/parameters/AD4_parameters.dat

I hope this helps,

Garrett

>
>
> Thanks in advance,
>
> Giulia
> ________________________________________________
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> ---

___
Dr Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon.)

The Scripps Research Institute,       tel: (858) 784-2292
Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
10550  North Torrey Pines Road,       email: garrett at scripps.edu
La Jolla,  CA 92037-1000,  USA.       mgl.scripps.edu/people/gmm






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