ADL: regarding active site

kaustubh kaustubh.joshi at systemsbiology.fi
Mon Jun 15 00:10:15 PDT 2009



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 
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