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pull down menu. • At first receptor protein should be imported then disable replace work space, fit to the screen and then import ligand into the workspace. • Click receptor tab in the panel and click the ligand in the work space. Green markers displayed on the ligand part. Now make sure that maestro has both ligand and receptor.
Pick the ligand manually – selects entry and click on ligand (ligand shows difference that it is selected) Click site tab. The enclosing box is shown in purple. Click centroid of selected residues (Note: for this you should know the active site residues) Specify residues manually by picking the residues or by selecting the residues (selecting the residues will be good) Go to sequence in selection box --- select your active sites amino acids and click add.
• In constraints tab. Click new. The gray sphere appears.Now click ok and see the pink color grid box found on receptor around your binding pocket.0 in the radius text box and click ok. thus new position dialogue box dialogue box opens. Thus the sphere changes to yellow. click positional tab. • Then enter 2. Click select residues button and choose active site residues of the protein or just click previous it will automatically accept the previous residues which we given as active site. Nik .
• The output file of the generated grid was in *. Nik . in that specify the working directory and file for storing output. • Manually with cursor pick your active site residues.zip format. ( it will help for flexible movement of active site residues to dock in good interaction level) • Amino acids selected will be shown star as it is selected. • Then start the job by clicking start button.Now go to Hbond Metal tab.
• In the docking section. which is present in the applications pull Down menu. For more rapid screening we can use HTVS option also. Nik . • Leave other default options as such. • In the Ligand tab.zip format. • A file selector opens. Glide runs Finish……. browse and choose the minimized structure of the ligand which prepared in lig prep.mae format and it shows the glide score for docked ligand and receptor. ensure that precission option is standard precision or XP or HTVS HTLS – Speed but not accurate SP and XP– Accurate but Time taken (XP will give good score). • In the Ligand Docking panel. • In the ligand docking-start panel we can specify the number of subjobs. • Glide results were visualized in interaction with protein and thereby Glide score was identified • Its output file was generated in glide_pv.Ligand docking ---------Select Ligand docking in the glide module. • This is the best choice for Docking large number of ligands. in that select the generated grid which was present in *. Out put -- Select pose viewer file • Then start the docking job.out. click the browse button in the receptor grid.