Here is a brief summary of the variable parameters for GeoFOLD. For more information, check out the reference (link).

keyword default value
Meaning
BREAKPOINTENTROPY 10. Entropy gained upon a break, in kJ/mol/degK
HINGEPOINTENTROPY 1. Entropy gained upon a hinge move, in kJ/mol/degK
PIVOTPOINTENTROPY 50. Entropy gained upon a pivot move, in kJ/mol/degK
TEMPERATURE 270. degK
OMEGA 13. Virtual denaturant. Lower omega = higher denaturant conc.
INTERMEDIATE 0 Number of the intermediate to follow during UnfoldSim
CONCENTRATION 1. Total protein concentration, in Mol/L
FOLDING 0 0 = unfolding, 1 = folding, in UnfoldSim
VOIDENTROPY 0. Entropy gained when a buried void space is exposed by unfoldinf. kJ/mol/degK
SOLIDITY 1000.
HBONDENERGY 1.
HAMMONDSCALE 1000. Hammond postulated that the tranition state lies towards the less stable ground state on the reaction coordinate. In this case, the reaction coordinate is the change in solvent accessible surface (SAS). The transition state position (theta-m) is defined for each unfolding step as the fraction of delta-SAS expressed at the t-state. The scale factor is a surface area H in A^2. Given H and the change in energy dNRG, theta-m is calculated as ( tanh( dNRG/ H) +1 ) /0.5
SIDECHAINENTROPY 1. Scale factor for sidechain entropy. Each amino acid has a different sidechain entropy, which is the difference in entropy between bound and fully solvent-exposed states. In this case, the amount of sidechain entropy expressed in a given unfolding step is equal to its intrisic entropy times the fraction of its total surface area exposed in that step.
HINGEBARRIER 0. Additional energy added to hinge transition states.

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