VMD-L Mailing List

From: denilson_at_dqi.ufla.br
Date: Tue Aug 27 2013 - 13:43:52 CDT

Dear Dehghan,

It seems to me that your work would be easier if you had chosen
AutodockTools to prepare your input files for calculation with Autodock.
That GUI was designed for that. At first, you will have to generate a
grid parameter file (gpf) to be used by Autogrid. Among other
informations, you will have to write in such gpf file the coordinates of
your grid box center (in Angstrons) and the size of your grid box (in
points). After the Autogrid calculation, which is very fast, you will
have to generate a docking parameter file (dpf) that will be used by
Autodock, together with the output of Autogrid. Both gpf and dpf can be
easily generated by Autodocktools.

Cheers.

Denilson

Denilson F. Oliveira
Laboratório de Produtos Naturais
Departamento de Química
Universidade Federal de Lavras
Caixa Postal 3037
Lavras (A CIDADE DAS QUEIMADAS) - MG - BRASIL
Fone: 55-35-3829-1623
Fax: 55-35-3829-1271
e-mail: denilson_at_dqi.ufla.br

-------- Mensagem original --------
Assunto: Re: vmd-l: VMD script
Data: Tue, 27 Aug 2013 11:29:58 -0500
De: John Stone <johns_at_ks.uiuc.edu>
Para: Axel Kohlmeyer <akohlmey_at_gmail.com>
CC: Marzieh Dehghan <M_Dehghan_at_ibb.ut.ac.ir>, vmd-l_at_ks.uiuc.edu

Marzieh,
   Most likely AutoDock doesn't use the same coordinate system
that you're assuming in your email below.

Cheers,
   John

On Sat, Aug 24, 2013 at 01:43:56PM +0000, Axel Kohlmeyer wrote:
> This looks like an autodock error and not a vmd issue.
>
> ------Original Message------
> From: Marzieh Dehghan
> Sender: owner-vmd-l_at_ks.uiuc.edu
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: VMD script
> Sent: Aug 24, 2013 1:54 AM
>
>
>
> hi every body,
>
> I am using VMD 1.9 and I have a problem. in order to determine center_x , y, z for docking, I used vmd script, after that the amount of x, y, z were obtained -4.59, 17.13, 12.29, respectively. after running autodock, I was confronted this error "search apace dimensions should be positive"
>
>
> I really appreciate if any one help me with this.
> Best Regards,
> Dehghan
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/