I have to write a code for docking. . I have two pdb. I have two write a protocol for moving the inhibitor towards trypsin until they touch. For the direction of the movement, to minimise the distance between the two, you can use the vector connecting the geometric centres of both,or movement along the x coordinate, then y coordinate,then z coordinate. Along the movement trajectory periodically check for the collision of the two,and stop when they collide/touch. the definition of the touch is 3 angstroms between the centre of any atom of trypsin and centre of any atom of the inhibitor. If the inhibitor moves too far and penetrates the trypsin,the procedure has to move it back,so there is no penetration just the surface contact. This will not put the inhibitor in the correct position. Find coordinates when the two touch. I have to write a code for this. Can someone please help me with this.
