Genetic Algorithm/Local Search Docking Parameters
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Section
Macromolecule and Ligand Files
Macromolecule
Grid Data File
Ligand
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Atom Types in Ligand
Model Internal Hydrogen Bonding: O-H
no
yes
N-H
no
yes
S-H
no
yes
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Ligand Starting State
Center of Ligand Molecule
Initial Translation of Ligand
user-defined
random
Initial Translation:
Initial Quaternion of Ligand
user-defined
random
Initial Quaternion:
Number of Dihedrals in Ligand:
Initial Relative dihedral angles of Ligand
user-defined
random
User-Specified Initial Dihedrals:
Number of Torsions Degrees of Freedom + Coefficient:
Specify Torsion Constraints?
yes
no
Number of Constraints on Torsions:
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Docking Run Parameters:
Number of GA-LS runs
Random Number Generator seed1
time
pid
user_defined
User-Defined Seed:
Random Number Generator seed2
time
pid
user_defined
User-Defined Seed:
Step Size:
Temperature(degrees)
Quaternion(degrees)
Dihedral(degrees)
Do Local Search :
no
only
do both
Number of Local Searchs to do:
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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
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Local Search Parameters
For local searchs, use
Solis & Wets with uniform variances
pseudo-Solis & Wets, with relative variances
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:
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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?
yes
no
Perform Cluster analysis on results based on final energies:
yes
no
Format for Output:
Output Level
no output
minimal output
full state output at end of each cycle
detailed output for each step
RMS (Root Mean Square Deviation) Calculations:
RMS value used for clustering:
Symmetry Checking in RMS calculations:
on
off
Reference file for RMS calculations:
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