Simulated Annealing Docking Parameters

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Macromolecule and Ligand Files

Macromolecule
Grid Data File
Ligand
There would be an applet here if your browser supported Java. Atom Types in Ligand
Model Internal Hydrogen Bonding: O-H N-H S-H
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Ligand Starting State

Center of Ligand Molecule
Initial Translation of Ligand
Initial Translation:
Initial Quaternion of Ligand
Initial Quaternion:
Number of Dihedrals in Ligand:
Initial Relative dihedral angles of Ligand
User-Specified Initial Dihedrals:
Number of Torsions Degrees of Freedom + Coefficient:
Specify Torsion Constraints?
Number of Constraints on Torsions:
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Docking Run Parameters:

Random Number Generator seed
User-Defined Seed for Random Number Generator
Step Size:
Temperature(degrees) Quaternion(degrees) Dihedral(degrees)
Reduction Factors Per Cycle:
Translation Quaternion
Dihedral Temperature
Initial Temperature(Degrees):
Job Parameters
Number of runs Number of cycles
Number of accepted steps per cycle Number of rejected steps per cycle
To begin next cycle, use state
Type of temperature reduction schedule to use:
Energy Parameters:
Energy assigned atoms outside the grid:(kcal per mole)
Energy Limit of Initial Random State Maximum Number of Retries
Calculate internal electrostatic energy?
Perform Cluster analysis on results based on final energies:
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Format for Docking Run Output:

Output Level
RMS (Root Mean Square Deviation) Calculations:
RMS value used for clustering:
Symmetry Checking in RMS calculations:
Reference file for RMS calculations:
Trajectory:
Output Trajectory?
Trajectory Output Frequency:
Begin Outputting Trajectory at cycle:
End Outputting Trajectory at cycle:
Trajectory output file:
For Trajectory, output
Create a Watch file:
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When all parameters are entered, click this button->