Make two PDB files: one with ligand and one with receptor
Type: setup grasp
Type: cp /eve/www/csb_home/userguides/graphics/grasp/defcol.dat .
Type: grasp
Click Right mouse button to get the main menu and then in the following sequence : Read |
PDB File | Show List
Select your ligand PDB file.
Click Right mouse button to get the main menu and then in the following sequence: Display | Alter |Bonds | Saved Set | Rods
Click Right mouse button to get the main menu and then in the following sequence: Set Parameters | Depth Cueing | Enter New Value | Bonds, Type: 1.2
Click Right mouse button to get the main menu and then in the following sequece: Set Parameters | System Miscellaneous | Bond Cylinnder Diameter, Type: 0.4
Click Right mouse button to get the main menu and then in the following sequece: Display | Alter | Bonds | Saved Set | Rods
Click Right mouse button to get the main menu and then in the following sequence : Read | PDB File | Show List
Select your receptor PDB file.
Click Right mouse button to get the main menu and then in the following sequence : Formal Subsets | Make a Formal Subset | Atoms | Make All Molecules Subsets | Use this one | Use this one
Click Right mouse button to get the main menu and then in the following sequence : Formal Subsets | Fix Dials to World (so you won't accidently move ligand relative to receptor)
Click Right mouse button to get the main menu and then in the following sequence : Set Parameters | System Miscellaneous | Minimum Surface Resolution, Type: 25
Click Right mouse button to get the main menu and then in the following sequence : Build | Molecular Surface | A Molecule | Molecule 1
Click Right mouse button to get the main menu and then in the following sequence : Build | Molecular Surface | A Molecule | Molecule 2 | Yes
Click Right mouse button to get the main menu and then in the following sequence : Calculate | Distance Array | A Surface to a Surface | A Constructed Surface | Surface 2 | A Constructed Surface | Surface 1
Type: vc=0, sub=m1
Type: vc=11, sub=m2
Type: vc=17, d=<1.4, sub=m2
Click Right mouse button to get the main menu and then in the following sequence : Miscellaneous | AntiAliasing (Polygons) and wait a minute.
When the picture smooths, Click Right mouse button to get the main menu and then in the following sequence : Write | RGB/Snapshot File, Type: filename.rgb