KIMMDY Hydrolysis Options
For all KIMMDY options see here.
cutoff
Cutoff distance [A] for the reaction. Water within this distance from the peptide bond will be considered for hydrolysis.
Type: float
Default: 6
step
Stepsize in frames for calculating the SASA (solvent accessible surface area) of each peptide bond and thus the reaction rate.
Type: int
Default: 1
kmc
KMC algorithm for this reaction.
Type: str
Options: [‘rfkmc’, ‘frm’, ‘extrande’, ‘extrande_mod’]
Default: rfkmc
ph_value
pH value of the system. The default value is 7.4. The rate of the reaction is scaled by the pH value. More basic conditions will increase the rate of the reaction.
Type: float
Default: 7.4
max_sasa
Maximum expeted solvent accessiblity of a C in a peptide bond. The reaction rate will be scaled based on the percent decrease of the SASA from this value. The default value is 3.97 A^2, which is the SASA of the C of the peptide bond in a simple glycine-glycine peptide.
Type: float
Default: 3.97
external_force
External force applied in nN. Note: 603 gromacs (kJ/mol/nm^2) units per strand are 1nN. The default (-1) means to calculate a force per bond based on bond extension using a morse potential. This needs PLUMED
Type: float
Default: -1
eq_bond_lengths
CSV file of equilibirum bond lengths for each peptide bond in the system. Colums: i,j,bond_length. The default is the empty string, in which case no equilibirum length correction is applied.
Type: str
temperature
Temperature
Type: float
Default: 310
theoretical_rates
For setting values in the arrhenius equation with rates based on theoretical energy calculations by Pill et al.
theoretical_rates.use
Use theoretical rates instead of empirical rates. The default is false.
Type: bool
Default: False
theoretical_rates.empirical_attempt_frequency
The attempt frequency in 1/ps with the default based on experiments by Pill et al.
Type: float
Default: 0.1
theoretical_rates.ts1
Energy barrier at 0 external force for TS1 of the hydrolysis reaction. [kJ/mol]
Type: float
Default: 80
theoretical_rates.ts2
Energy barrier at 0 external force for TS2 of the hydrolysis reaction.
Type: float
Default: 92
theoretical_rates.ts1_force_scaling
Force scaling factor for TS1 in kJ/mol/nN
Type: float
Default: 1.67
theoretical_rates.ts2_force_scaling
Force scaling factor for TS2 in kJ/mol/nN
Type: float
Default: 25.83
theoretical_rates.critical_force
Force in nN at which (the activation energy of) TS2 becomes lower than TS1 and this TS1 becomes the rate limiting step.
Type: float
Default: 0.7