ADL: regarding active site

Bagdevi bagdevi.mishra at gmail.com
Mon Jun 15 01:42:39 PDT 2009


Can you locate 3DM2.gpf in your working directory. Your details
regarding grid must be specified in it. And are you running autogrid4
using this gpf file.


Regards,
Bagdevi Mishra.




On Mon, Jun 15, 2009 at 12:40 PM,
kaustubh<kaustubh.joshi at systemsbiology.fi> wrote:
>
>
> Dear Stefano, Bagdevi,
>                                   I did tried to follow your instructions,
> but in all the cases i failed totally. Main problem I found is the grid is
> not generated at the point I am specifying.
> For example I am attaching a protein structure and a ligand.
> For this system, the active site includes residues 100, 103, 105, 179,181,
> 188,190, 227.
> I tried by different ways to assign the grid occupying all these residues,
> but none of the methods worked. Instead the grid generation and docking
> respectively take place at another position (viz. residues 332,419,420,421)
> which are located at the surface of protein and quite distinct from the
> expected active site.
> Could some body try a quick run on this system and explain with method
> followed how to approach right docking.
>
>
> Thanks in advance
>
> Kaustubh
>
>
> http://n2.nabble.com/file/n3078883/3DM2.pdb 3DM2.pdb
> http://n2.nabble.com/file/n3078883/8.pdbqt 8.pdbqt
> --
> View this message in context: http://n2.nabble.com/regarding-active-site-tp3066853p3078883.html
> Sent from the AutoDock mailing list archive at Nabble.com.
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


More information about the autodock mailing list