|
|
Residue Scanning - Advanced Options Dialog Box |
Set options for affinity maturation: the effective temperature of the simulation, the seed for random number generation, options for accepting or rejecting moves or terminating the calculation. Also add an implicit solvent membrane if desired.
To open the Residue Scanning - Advanced Options dialog box, you can:
Click Advanced in the Options tab of the Residue Scanning panel.
Calculate the change in acidity of the mutated residues, using PROPKA.
Use a membrane model that is defined by a low-dielectric slab in which the protein is placed. The exterior of the slab has the usual high-dielectric implicit solvent.
Click this button to define the implicit solvent membrane and place the protein in the membrane. Opens the Prime Membrane Setup panel.
Set the effective temperature for the Monte Carlo walk, where the acceptance probability is the usual Boltzmann-type factor, with the change in the MM-GBSA energy in the exponent.
If no mutation is accepted in the specified number of moves (mutations), stop the calculation and return the results. This option prevents the calculation from spending a lot of time when there is no new acceptable mutation to be found.
Specify the random number seed for selecting the mutation to perform at each step.
If the stability changes at a given step by more than the specified amount when the affinity is being optimized, reject the step.
If the affinity changes at a given step by more than the specified amount when stability is being optimized, reject the step. Only applicable if the protein has been divided into two sets of chains.
|