MM-GBSA 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 this dialog box, click Advanced in the MM-GBSA Residue Scanning Panel.
- Features
- Additional Resources
MM-GBSA Residue Scanning - Advanced Options Dialog Box Features
- Report changes in pKa option
- Use implicit solvent membrane option
- Define Membrane button
- Effective temperature text box
- Terminate calculation if no new accepted move found in n moves option and text box
- Random number seed text box
- When optimizing affinity, reject steps with stability change > N option and text box
- When optimizing stability, reject steps with affinity change > N option and text box
- Report changes in pKa option
-
Calculate the change in acidity of the mutated residues, using PROPKA.
- Use implicit solvent membrane option
-
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.
- Define Membrane button
-
Click this button to define the implicit solvent membrane and place the protein in the membrane. Opens the Prime Membrane Setup Panel.
- Effective temperature text box
-
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. As this energy typically overestimates the affinity changes due to mutation by a factor of 2-5, an effective temperature of 600-900K should improve the exploration of sequence space.
- Terminate calculation if no new accepted move found in n moves option and text box
-
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.
- Random number seed text box
-
Specify the random number seed for selecting the mutation to perform at each step.
- When optimizing affinity, reject steps with stability change > N option and text box
-
If the stability changes at a given step by more than the specified amount when the affinity is being optimized, reject the step.
- When optimizing stability, reject steps with affinity change > N option and text box
-
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.