Simulated Annealing Docking Parameters
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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:
Random Number Generator seed
time
pid
user_defined
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
minimum
last
state
Type of temperature reduction schedule to use:
linear
geometric
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
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Format for Docking Run 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:
Trajectory:
Output Trajectory?
yes
no
Trajectory Output Frequency:
Begin Outputting Trajectory at cycle:
End Outputting Trajectory at cycle:
Trajectory output file:
For Trajectory, output
accepted steps
accepted AND rejected steps
Create a Watch file:
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