Schrodinger procedure

Import the pdb structure

Projectimport structure ok

Protein preparation
Workflows protein preparation wizard: preprocess, optimize, minimize

Receptor grid generation

Applications glidereceptor grid generation
Receptor tab:
Uncheck pick to identify ligand, select specify for selected residues click on select and add
residue number click on add ok
Site tab:
Select centroid of selected residue click specify residue select add the residue
numberadd ok
Click Start from receptor grid generation pop up window

Ligand preparation
Applicationsligprep browse the ligand file in SDF formatclick on output format SDF

Docking (HTVS mode)

Applicationsglideligand docking
Browse the receptor grid file select HTVS
LIGAND TAB: browse ligand sdf file (ligprep o/p or sdf file)
OUTPUT TAB: check write per residue interaction score AND compute RMSD
And click on start
(After finishing job) project  close  discard
Project  import structure (open pv.maegz file (output of htvs))
Project show table analyze docking score or glide Gscore (both are identical)
Table:  exportstructuressave in sdf format
LIGPREP (same as previous steps)

Docking (XP mode)

Applicationsglideligand docking
Browse the receptor grid file click on XP (extra precision)
Check writes XP descriptors
LIGAND TAB: browse the output file of ligprep in sdf format (from c:/documents and
settings/admin)
OUTPUT TAB: check write per residue interaction score AND compute RMSD
And click on start
(After finishing job) project  close  discard
Applications glide xp visualizer open xpds.maegz file
OR Project  import structure (open xpds.maegz file (XP output))
Project show table analyze docking score or glide Gscore(both are identical)
Table:  exportstructuressave in sdf format