ADL: GRID.. problems

Tee Pioj tee_piorj at yahoo.com
Sat Mar 1 21:29:02 PST 2008


hi! Antonio Cavazzuti 
talking about setting up grid. because of a difference in coordinate of ligand and macromolecule, it make ligand far from moromolecule. The solution is to find center of binding site. You can do that by using pdbcen command coming with autodock package. What you should do is knowing about the component of binding site, then edit file by deleting non-active site component and save as another name in any format ( .txt, .pdb). After that, use pdbcen command as following:

(your working directory) pdbcen yourfilename  

you will get coordinate of active site, then put these no. in grid dialogue box (in Autodock tools). It will appear a cubic box around that coordinate (active site) but don't worry if the ligand stands still. Autodock is automated docking, the ligand will finally move to active site you have assigned. 

Best luck,
Tee Piroj

----- Original Message ----
From: Antonio Cavazzuti <acavazzuti at ipb.csic.es>
To: autodock at scripps.edu
Sent: Sunday, March 2, 2008 9:58:09 AM
Subject: ADL: GRID.. problems

Hi,
I have some problem in setting up the grid: when I open autodock4 result, I
see that conformers have been originated about 40Å far from active site.. The
grid doesn't appear where I wanted.. 
Any suggestion about where to find informations about 'fld
1d6o_3_rigid.maps.fld', 'Coordinates of Central Grid Point of Maps', 'Grid
Parameter file used to create Grid Maps' and 'Minimum/Maximum coordinates in
grid' meaning?
Thanks very much,
Antonio

Instituto de Parasitologia y Biomedicina "Lopez-Neyra"
Avda. Conocimiento S/N
Parque Tecnologico Ciencias de la Salud
18100 Armilla - GRANADA
Spain
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Fax: 958181632
http://www.ipb.csic.es
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