How to define a grid box for a particular motif of a protein.
For defining a grid box, we need coordinates, from where can we get that?
I tried to get the coordinates from different servers (cast-p, pocket finder, lig site). When we use the coordinated generated from the same, autodock was giving error like "Unable to open rigid S.A rigid Map"
First you should get the grid center coordinate, i.e. pick up in the pdb file the coordinates of the center atom of your motif. Then run autogrid with this coordinate in your input script.
Do we have any online software which can get me the coordinate, which i may define it in autodock?
i have tried autodock, it demands grid coordnates.. This is what the problem is :(
Try to create grid on the basis of coordinates of active site of protein
Going through the tutorials would sound reasonable:
http://autodock.scripps.edu/faqs-help/tutorial
Dear Chawla,
Initially try to translate and rotate the protein and find your motif or active site. In defining the grid box, you can see "pick an atom" or "Center on atom" something like this at the top of the grid dialogue box. Now you can adjust the spacings in x, y and z direction so as to construct a reasonable box. Finally, don't forget to click "Close saving current selection" . Bye
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