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Glide Steps

Glide Steps

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Publicado porselnikraj

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Published by: selnikraj on Nov 26, 2010
Direitos Autorais:Attribution Non-commercial


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Import both ligand and receptor in maestro working panel • Select Glide - Receptor grid generation in the applications

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.


click positional tab. The gray sphere appears. • In constraints tab. 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. Click new. Thus the sphere changes to yellow.0 in the radius text box and click ok. thus new position dialogue box dialogue box opens. • Then enter 2.Now click ok and see the pink color grid box found on receptor around your binding pocket. Nik .

• The output file of the generated grid was in *. • Then start the job by clicking start button.Now go to Hbond Metal tab. in that specify the working directory and file for storing output. Nik .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. • Manually with cursor pick your active site residues.

• In the Ligand tab. Nik . • Glide results were visualized in interaction with protein and thereby Glide score was identified • Its output file was generated in glide_pv. • This is the best choice for Docking large number of ligands. Out put -- Select pose viewer file • Then start the docking job. in that select the generated grid which was present in *.mae format and it shows the glide score for docked ligand and receptor. • In the Ligand Docking panel. Glide runs Finish……. • In the docking section. which is present in the applications pull Down menu.zip format.Ligand docking ---------Select Ligand docking in the glide module. For more rapid screening we can use HTVS option also. • Leave other default options as such. • A file selector opens. click the browse button in the receptor grid. browse and choose the minimized structure of the ligand which prepared in lig prep.out. • In the ligand docking-start panel we can specify the number of subjobs. 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).

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