# SIMULATION PARAMETERS FILE ## ---- General simulation parameters ---------- SIMMETHOD SimulatedAnnealing #"Genetic" or "SimulatedAnnealing" for simulated annealing (default) or "ReplicaExchange" for replica exchange STEPS 75000 #default 100; how many simulation steps to perform? ANNTEMP 10 #from range X to Y REHEAT false 1 #REPLICAEXCHANGE_FREQ 2 #each X steps replicas will be exchanged; by default every 10% of simulation steps #REPLICATEMPERATURES 200 100 50 0 # 400 375 350 325 300 275 250 225 200 175 150 125 100 #list of temperatures for all replicas MAXROT 5 #default is 5 MAXTRANS 5 5 5 #default is [5, 5, 5] ## --- Scoring function parameters ---------- OUTBOX 1 1 #default 1 1; can be in range from 0 to 10 (float numbers) MAP_FREESPACE 0 0 #default 1 1; can be in range from 0 to 10 (float numbers) CLASHES 1 1 #default 1 1; can be in range from 0 to 10 (float numbers) RESTRAINTS 0 0 #default 1 1; can be in range from 0 to 10 (float numbers) DENSITY 3 3 #default 1 1; can be in range from 0 to 10 (float numbers) ### ---- Mutation frequencies ----------- ROTATION_FREQ 0.45 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1 ROTATION_COV_FREQ 0.0 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1 TRANSLATION_FREQ 0.45 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1 EXCHANGE_FREQ 0.05 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1 SIMUL_DD_FREQ 0.0 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1 TRANSLATION_ALL_FREQ 0.025 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1; mutation were all components are translated together ROTATION_ALL_FREQ 0.025 #from range 0 to 1, default is 0.25, sum of FREQ params must be equal to 1; mutation were all components are translated together ## ----- Input data descriptors -------- #THRESHOLD 1.6 #float value existing in map file, default is 0 KVOL 1.0 SIMBOX 1.2 #default simulation box diameter GRIDRADIUS 1.6 #default is 1.0 GRIDTYPE cubic #cubic or diamond COMPONENT_REPRESENTATION fa #CA - only calfas/c4' (default); cacb - coarse grain, 3p - 3points, fa - full atom ### ----- Simulation process control ------- SCALEPARAMS on #on/off PARAMSCALINGRANGES 0 25 50 #default 0 25 50; at what point of simulation should parameter scaling ranges kick in; % zakresu symulacji (postep) PARAMSCALINGR1 50 100 #default 50 100 in % PARAMSCALINGR2 25 50 #default 25 50 in % PARAMSCALINGR3 0 25 #default 0 25 in % ## ------ Output parameters --------- #WRITE_N_ITER 1 #default 0, minimum 1 max=STRUCT_NR WRITE_EACHBETTER True #OUT_STEPS 10 15 #default one struct with best score; which steps in output data? #STRUCT_NR 14 #default 0.1*SIMUL_NR; number ot out structure with best scores #COMPONENTS MOVEMENTS INFORMATION #MOVE_STATE A fixed #MOVE_STATE X_protein fixed #MOVE_STATE D movable 5 5 5 0.1 0.1 0.1 10 10 10 0.1 0.1 1 5 30 #max_rot_angle; axis *3; maxtrans, sum_rots, sum_trans, around_line rot_single, rot_sum #MOVE_STATE D movable 5 5 5 0.1 0.1 0.1 180 180 180 1 1 1 5 90 #max_rot_angle; axis *3; maxtrans #MOVE_STATE Z movable 5 5 5 0.1 0.1 0.1 180 180 180 1 1 1 5 90 #max_rot_angle; axis *3; maxtrans #START_ORIENTATION true #True if user sets start conformation, False if not!! #define components that are mutated together; eg. A [Z,D] if A is rotated/translated then Z and D will be also rotated/translated #COVALENT_BONDS A ['Z','D'] [10,'CA'] [11,'CA'] #to indicate which components are covalently bonded #COVALENT_BONDS A ['D'] [5,'CA'] [7,'CA'] #COVALENT_BONDS D ['A'] #to indicate which components are covalently bonded #COVALENT_BONDS Z ['A'] [14,'CA'] [15,'CA'] #to indicate which components are covalently bonded #COVALENT_BONDS A [B] #to indicate which components are covalently bonded #COVALENT_BONDS B [A,C] #to indicate which components are covalently bonded #COVALENT_BONDS C [B] #to indicate which components are covalently bonded #COVALENT_BONDS D [E,F] #to indicate which components are covalently bonded #COVALENT_BONDS E [D] #to indicate which components are covalently bonded #COVALENT_BONDS F [D] #to indicate which components are covalently bonded # EXAMPLES #use density map equal to 10 complex volumes #KVOL 10 #use density map with density values >= threshold equal to 1.5 #THRESHOLD 1.5 #perform only 5 simulation steps #STEPS 5 #perform default number of steps #STEPS X #“give me the structure with best score” #OUT_STEPS FIRST LAST #STRUCT_NR 1 #“give me structures with 100 best scores” #OUT_STEPS FIRST LAST #STRUCT_NR 100 #“give me all structures from the part of trajectory, steps: 13548-13570” #OUT_STEPS 13548 13570 #STRUCT_NR 22 #“give me the structure with 7th best score among all structures #from the part of trajectory, steps: 13548-13570” #OUT_STEPS 13548 13570 #STRUCT_NR 7