Genetic Algorithm/Local Search Docking Parameters

Go to: Section

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
Go to: Section

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:

Go to: Section

Docking Run Parameters:

Number of GA-LS runs
Random Number Generator seed1 User-Defined Seed:
Random Number Generator seed2 User-Defined Seed:
Step Size:
Temperature(degrees) Quaternion(degrees) Dihedral(degrees)
Do Local Search : Number of Local Searchs to do:
Go to: Section

Genetic Algorithm Parameters

Population size Maximum Number of energy evaluations
Maximum Number of generations
Number of top individuals that automatically survive
Rate of Gene Mutation
Rate of Crossover
Number of generations for picking worst individual
Mean of Cauchy distribution for gene mutation
Variance of Cauchy distribution for gene mutation

Go to: Section

Local Search Parameters

For local searchs, use
Maximum number of iterations
Maximum number of successes in a row before changing rho
Maximum number of failures in a row before changing rho
Solis & Wets parameter defining initial variance and size of local space to sample:
Lower bound on rho:
Probability of any particular phenotype being subjected to local search:

Go to: Section

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:

Format for Output:

Output Level
RMS (Root Mean Square Deviation) Calculations:
RMS value used for clustering:
Symmetry Checking in RMS calculations:
Reference file for RMS calculations:

Go back to: Section

When all parameters are entered, click this button->