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 |