ADL: GRID.. problems II (Antonio Cavazzuti)

Antonio Cavazzuti acavazzuti at
Thu Mar 6 07:47:48 PST 2008

Hi , Thanks for the answer.
I tried using pdbcen, but when I launch the command the answer is "command not
found". I lauched the command from directory where files were generated..
I'm working with Autodock4 with Ubuntu 7.10. I'm sure that the solution is
easy, but I don't know where to look for :)

>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

>Best luck,
>Tee Piroj

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

>>I have some problem in setting up the grid: when I open autodock4 result, I
>>see that conformers have been originated about 40? 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,

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