Here is a brief summary of the variable parameters for GeoFOLD.
For more information, check out the reference (link).
Also see How to Read Geofold Output.
| keyword | default value |
|
|
| VOIDENTROPY | 0. | Entropy assigned to a void space. (Turned off by default) Entropy is realized when the set of residues holding the void is broken. | U |
| SOLIDITY | 1000. | Surface area burial (A^2) below which protein becomes more like a liquid. Unfolding entropy limits to zero as surface area burial limits to zero. | U |
| HBONDENERGY | 1000. | kJ/mol per hydrogen bond. Only backbone H-bonds are modeled. | U |
| HINGEBARRIER | 0. | Optional additional barrier for hinge moves. | U |
| PIVOTBARRIER | 0. | Optional additional barrier for pivot moves. | U |
| ORANGE | 5. 10. 20. 30. | Omega range. List any number of OMEGA values (surface tension. virtual urea). UnfoldSim will run using each of the listed omega values. | U |
| HALFLIFE | 0 |
End this simulation at the halfway point. 1 = stop folding when [F] >= 1/2 stop unfolding when [U] >= 1/2 0 = run UnfoldSim to convergence. |
U |
| MAXSPLIT | 4 | Maximum number of elemental unfolding steps applied to one intermediate. Optional values are 2,4,8,16, and 32. Speed is effected by higher settings. | G |
| REDUCING | 0 |
0 = oxidizing conditions. Disulfides identified by the program will be inflexible. 1 = reducing conditions. Disulfides are treated as free cysteines. |
G |
| RUNGEOFOLD | 1 |
1 = Run GeoFold over again in the re-run. This should be set to 1 if any GeoFold variables have been changed. 0 = Do not re-run GeoFold. Use the previous run. Only re-run UnfoldSim. Any changed GeoFold variables will be ignored. |
G,U |
| MAXTIME | 10. | Maximum extent of a UnfoldSim simulation, in seconds. A simulation will stop earlier if convergence is reached or if HALFLIFE is set and the halflife is reached. | U |
| MINSEG | 4 | Smallest piece of the chain that can be pivoted. Setting this number too high may cause an pivot point to be missed. Setting it too small causes the protein to unfold by peeling from one end. | G |
| BREAKPOINTENTROPY | 90. |
Entropy gained upon a break, in kJ/mol/degK. A break is the separation of two unconnected segments or chains. |
U |
| HINGEPOINTENTROPY | 30. |
Entropy gained upon a hinge move, in kJ/mol/degK A hinge is the rotation of a segment around two points located at either end of the rotating segment. |
U |
| PIVOTPOINTENTROPY | calculated |
Entropy gained upon a pivot move, in kJ/mol/degK. A pivot is the rotation of a segment around a single point, in any direction. This entropy must be the average of BREAKPOINTENTROPY and HINGEPOINTENTROPY, because entropy is a state function and 2 pivots of unfolding can arrive at the same state as one break and one hinge. |
U |
| TEMPERATURE | 270. | Temperature in degrees Kelvin. | U |
| OMEGA | 13. | Virtual denaturant. Lower omega means higher denaturant conc. Units are kJ/mol/Å2 | U |
| INTERMEDIATE | 0 | Identifier number of the intermediate to track during UnfoldSim runs. (default: none) | U |
| CONCENTRATION | 1. | Total protein concentration, in Mol/L, to be assigned to the system. If the protein is an oligomer, then this concentration may affect the unfolding pathway. Otherwise, it has no effect. | U |
| FOLDING | 0 | 0 = unfolding, 1 = folding. The direction of the simulation in UnfoldSim. | U |
| VOIDENTROPY | 0. | Entropy gained when a buried void space is exposed by unfolding, in kJ/mol/degK. | U |
| SOLIDITY | 1000.Å2 | When the total buried surfae of an intermediate is less than SOLIDITY, the intermediate is treated as a liquid, otherwise it is a solid. For a solid, the entropy of unfolding is expressed after the transition state. For a liquid, it is expressed before the transition state. | U |
| HAMMONDSCALE | 1000. | Hammond postulated that the tranition state lies closer to the higher energy ground state on the reaction coordinate. The reaction coordinate in GeoFold is the solvent accessible surface area (SAS). The transition state position (theta-m) is defined for each unfolding step as the fraction of delta-SAS expressed at the t-state. HAMMONDSCALE (H) is in units of surface area Å2. The location of the transitions state, theta-m = ( tanh( dNRG/ H) +1 ) /0.5 | U |
| 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. | U |
| BREAKCUT | 0.2 | If a substructure contains two chain segments, either because the protein is oligomeric or because a hinge operation has created two chain segments, and these segments can be separated by a simple translation without collisions in at least BREAKCUT = 0.05 of all possible directions, then a break exists and the two chain segments are labeled u1 and u2. | G |
| PIVOTCUT | 0.01 | A point on the chain is a pivot point if the segment N-terminal to it can rotate 30 degrees without collision in PIVOTCUT of all possible directions. If so, then then the N-terminal and C-terminal segments are labeled u1 and u2. | G |
| HINGECUT | 0.5 | Two points on the chain define a hinge motion if the intervening atoms can rotate at least a total of HINGECUT * 60 degrees without collision. If so, then the intervening segment is labeled u2 and the rest if labeled u1, and u1 has two parts to it which may separate by a Break move. | G |