Difference between revisions of "2022 DOCK tutorial 3 with PDBID 1X70"
BrockBoysan (talk | contribs) (→Surface Generation & Spheres) |
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To generate spheres make the following input file: | To generate spheres make the following input file: | ||
"INSPH" - | "INSPH" - | ||
| − | 1X70_dms.dms #Molecular Surface File | + | 1X70_dms.dms #Molecular Surface File |
| − | R #Whether to generate spheres outside of surface (R) or inside (L) | + | R #Whether to generate spheres outside of surface (R) or inside (L) |
| − | X #Surface points from the DMS file to use in sphere generation | + | X #Surface points from the DMS file to use in sphere generation |
| − | 0 #Minimum radius between spheres | + | 0 #Minimum radius between spheres |
| − | 4.0 #Maximum radius of sphere | + | 4.0 #Maximum radius of sphere |
| − | 1.4 #Minimum radius of sphere | + | 1.4 #Minimum radius of sphere |
| − | 1X70_wo_H.sph #Output sphere file | + | 1X70_wo_H.sph #Output sphere file |
End of File (EOF) | End of File (EOF) | ||
Revision as of 17:45, 28 February 2022
Contents
Introduction
DOCK
System Preparation
Fetching 1X70 Open Chimera: File > Fetch By Id > 1X70
Surface Generation & Spheres
This section details the generation of sphere files which will be used to describe where you are trying to DOCK to on your protein.
Surface Generation In Chimera: Load 1X70 w/o Hydrogens > actions > show > surface
Then you will write a DMS (Molecular Surface) File With the surface generated in Chimera: Tools > Structure Editing > Write DMS
Now you should have a DMS file for the next step.
Sphere Generation To generate spheres make the following input file: "INSPH" -
1X70_dms.dms #Molecular Surface File R #Whether to generate spheres outside of surface (R) or inside (L) X #Surface points from the DMS file to use in sphere generation 0 #Minimum radius between spheres 4.0 #Maximum radius of sphere 1.4 #Minimum radius of sphere 1X70_wo_H.sph #Output sphere file
End of File (EOF)
For more information on sphere generation see: https://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
The .sph file should give you something similar to the following image if you load it up over your protein in Chimera:
Sphere Selection
Making The Infamous Grid
Making the grid
Energy Minimization for the ligand
Docking & Virtual Screening
Rigid Docking
Fixed Anchor Docking
Flexible Docking
Placeholder
[[File:|thumb|center|800px|image placeholder]]
