Table 3 C-Docker docking protocol parameters
Parameters | Inputs |
|---|---|
Input receptor | ../Input/3NT1.dsv |
Input ligands | C:\Users\g\Desktop\all 55 new.sd |
Input site sphere | −40.4058, −51.8288, −22.5019, 8.50067 |
Top hits | 1 |
Random conformations | 10 |
Random conformations dynamics steps | 1000 |
Random conformations dynamics target temperature | 1000 |
Include electrostatic interactions | True |
Orientations to refine | 10 |
Maximum bad orientations | 800 |
Orientation VDW energy threshold | 300 |
Simulated annealing | True |
Heating steps | 2000 |
Heating target temperature | 700 |
Cooling steps | 5000 |
Cooling target temperature | 300 |
Force field | CHARMm |
Use full potential | TRUE |
Grid extension | 8 |
Ligand partial charge method | CHARMm |
Random number seed | 314,159 |
Final minimization | Full potential |
Random dynamics time step | 0.002 |