VMD-L Mailing List

From: denilson_at_dqi.ufla.br
Date: Wed Aug 28 2013 - 06:51:11 CDT

Hi Nuno.

Sorry. I did not know about Vslab plugin for VMD.

Best wishes.

Denilson.

Prof. 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

Em 27-08-2013 17:52, Nuno Sousa Cerqueira escreveu:
> Hello Dehghan,
>
> Did you follow my instructions to use vslab ( autodock plugin for VMD).
> Did it work well ?
>
> Regards,
>
> Nuno M. F. Sousa A. Cerqueira
> Assistant Researcher
> Faculdade de Ciências
> Universidade do Porto
> Portugal
>
> No dia 27/08/2013, às 20:43, "denilson_at_dqi.ufla.br
> <mailto:denilson_at_dqi.ufla.br>" <denilson_at_dqi.ufla.br
> <mailto:denilson_at_dqi.ufla.br>> escreveu:
>
>> 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 Kohlmeyerakohlmey_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/
>>
>>
>>