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run.prm.quick
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run.prm.quick
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MCCE CONFIGURATION FILE (Quick 05/29/2009)
EDITED TO BE REALLY QUICK 5/16/2014 by MRG
This file must have name "run.prm" in the working directory. The first
field of the line is the value, and last string with parenthesis is
the key.
You need this configure file in your working directory.
You need to point out a pdb file to work on.
Optionally:
You may need file defined by "RENAME_RULES" to customize cofactors.
You may need file defined by "EXTRA" to customize advanced contols.
==============================================================================
Most modified entries
------------------------------------------------------------------------------
Input and Output:
prot.pdb (INPDB)
Steps:
f step 1: pre-run, pdb-> mcce pdb (DO_PREMCCE)
f step 2: make rotatmers (DO_ROTAMERS)
f step 3: do energy calculations (DO_ENERGY)
f step 4: monte carlo sampling (DO_MONTE)
f step 6: Hydrogen bond analysis (DO_ANALYSIS)
==============================================================================
0 sidechain optimization: 0=mcce, 1=P.Comte's GA, (SIDECHAIN_OPT)
2=mcce + MHD's pruning function
delphi Poisson-Boltzmann solver,apbs or delphi (PBE_SOLVER)
surface self/surface, APBS always use rxn self energy (RXN_METHOD)
==============================================================================
Less modified entries
------------------------------------------------------------------------------
4.0 Protein dielectric constant for DelPhi (EPSILON_PROT)
/home/mcce/Stable-MCCE/extra.tpl (EXTRA)
/home/mcce/Stable-MCCE/name.txt MCCE renaming rule. (RENAME_RULES)
ph "ph" for pH titration, "eh" for eh titration (TITR_TYPE)
0.0 Initial pH (TITR_PH0)
1.0 pH interval (TITR_PHD)
0.0 Initial Eh (TITR_EH0)
30.0 Eh interval (in mV) (TITR_EHD)
15 Number of titration points (TITR_STEPS)
=============================================================================
#############################################################################
MODIFYING FOLLOWING ENTRIES REQUIRE ADVANCED KNOWLEDGE:
-----------------------------------------------------------------------------
/home/mcce/Stable-MCCE (MCCE_HOME)
t Minimize output files (MINIMIZE_SIZE)
t Print trace file (DO_TRACE)
Options specific to each step:
step 1:
t Label terminal residues? (TERMINALS)
2.0 distance limit of reporting clashes (CLASH_DISTANCE)
0.05 cut off water if % SAS exceeds this number (H2O_SASCUTOFF)
t ignore hydrogens in input structure (IGNORE_INPUT_H)
#turning ignore input h to f may cause error in rotatmer making
step 2:
f Use specific control (head1.lst) on rotamer making (ROT_SPECIF)
t Out ms_gold file for Microstate selection (MS_GOLD_OUT)
t Do swap (stereo isotope) (ROT_SWAP)
f Do rotate? (PACK)
0 number of rotamers in a bond rotation (ROTATIONS)
1.00 SAS Threshold not making rotamers (SAS_CUTOFF)
10.0 Cutoff of self vdw in kcal/mol (VDW_CUTOFF)
5000 number of repacks (REPACKS)
0.01 occupancy cutoff of repacks (REPACK_CUTOFF)
f h-bond directed rotamer making, requir 't' on Do rotate (HDIRECTED)
1.0 threshold for two conformers being different (HDIRDIFF)
36 Limit number of the Hbond conformers (HDIRLIMT)
0 number of cycles to relax rotamer clash (HV_RELAX_NCYCLE)
4 time (in fs) for each relaxation iteration (HV_RELAX_DT)
100 number of iterations (HV_RELAX_NITER)
2. relax rotamer if vdw interaction is bigger than this (HV_RELAX_VDW_THR)
10. not relax rotamer if heavy atom vdw is bigger than this (HV_RELAX_HV_VDW_THR)
20. scaling factor for torsion during relaxation (HV_TORS_SCALE)
10000 maximun n steps of shake (HV_RELAX_N_SHAKE)
1.0 constraint distance (HV_RELAX_CONSTRAINT)
20. constraint force for atom stay in original position (HV_RELAX_CONSTRAINT_FRC)
-2.0 relax if electrostatic interaction is more favorable than this, and the charged groups are close (HV_RELAX_ELEC_THR)
0.3 threshold used to define a charged atom, see hv_relax_elec_dist_thr (HV_RELAX_ELEC_CRG_THR)
2.0 only relax electrostatically favorable pairs that has charged atom distance shorter than this (HV_RELAX_ELEC_DIST_THR)
f Do relaxation on hydrogens (RELAX_H)
-1.0 Energy threshold for keeping the conformer (RELAX_E_THR)
100 Loop over N local microstates (RELAX_NSTATES)
36 default number of hydroxyl positions (RELAX_N_HYD)
5. do not relax hydrogen if vdw bwt two sidechain conformer bigger than this (RELAX_CLASH_THR)
1.0 phi for each step of relaxation (RELAX_PHI)
300 Maximum number of steps of relaxation (RELAX_NITER)
0.5 Torque threshold for keep relaxing (RELAX_TORQ_THR)
step 3:
80.0 Solvent dielectric constant for DelPhi (EPSILON_SOLV)
65 Grids in each DelPhi (GRIDS_DELPHI)
2.0 The target grids per angstrom for DelPhi (GRIDS_PER_ANG)
1.4 Radius of the probe (RADIUS_PROBE)
2.0 Ion radius (IONRAD)
0.15 Salt (SALT)
/home/mcce/Stable-MCCE/bin/delphi DelPhi executable (DELPHI_EXE)
/home/mcce/mcce2.5.1/bin/apbs APBS executable (APBS_EXE)
step 4:
f Output Microstate from standard monte carlo (MS_OUT)
f Output readable micristate file from standard monte carlo (RE_MS_OUT)
5.0 Big pairwise threshold to make big list (BIG_PAIRWISE)
-1 Random seed, -1 uses time as random seed (MONTE_SEED)
298.15 Temperature (MONTE_T)
3 Number of flips (MONTE_FLIPS)
100 Annealing = n_start * confs (MONTE_NSTART)
300 Equalibration = n_eq * confs (MONTE_NEQ)
0.001 Cut-off occupancy of the reduction (MONTE_REDUCE)
6 Independent monte carlo sampling (MONTE_RUNS)
2000 Sampling = n_iter * confs (MONTE_NITER)
50000 Trace energy each MONTE_TRACE steps, 0 no trace (MONTE_TRACE)
1000000 Maximum microstates for analytical solution (NSTATE_MAX)
t Do entropy correction (MONTE_TSX)
f Specify mfe point, f=pKa/Em (MFE_POINT)
-1.0 MFE cutoff(Kcal), default 0.5 (MFE_CUTOFF)
Step 6:
t Obtain hydrogen bond matrix (GET_HBOND_MATRIX)
1.2 Lower limit of hydrogen bond H--B distance (HBOND_LOWER_LIMIT)
3.2 Upper limit of hydrogen bond H--B distance (HBOND_UPPER_LIMIT)
90.0 Angle cutoff of hydrogen bond (HBOND_ANG_CUTOFF)
t Obtain hydrogen bond network (GET_HBOND_NETWORK)
# Advanced options:
1 delphi start conformer number, 0 based (PBE_START)
99999 delphi end conformer number, self included (PBE_END)
/scratch delphi temporary file folder, "/tmp" uses node (PBE_FOLDER)
6.0 dielectric constant for Coulomb's law (EPSILON_COULOMB)
##############################################################################
#APBS
65 number of grids (GRIDS_APBS)
mol protein-solvent surface definition: mol/smol/spl2/spl4 (SURFACE_APBS)
spl0 mapping the point charges to the grid: spl0/spl2/spl4 (CHARGES_APBS)
sdh type of PBE boundary condition: zero/sdh/mdh/focus (BOUND_COND_APBS)
##############################################################################
###########PASCAL COMTE GENETIC ALGORITHM PARAMETERS FOR STEP 2################
-1 Random seed value, use -1 for random value (GA_SEED)
6000 Population size of each GA: use up to 20k (GA_POP_SIZE)
0.1 Mutation rate for each GA (GA_MUTATION_RATE)
0.0 Migration rate for each GA (GA_MIGRATION_RATE)
0.9 Crossover rate for each GA (GA_CROSSOVER_RATE)
30 Max nb. of rnd cut points for crossover (GA_RANDOM_CUT_POINTS)
10 Nb. of GA rounds without convergence check (GA_PHASE)
5 Nb. of GA rounds with convergence check (GA_SHIFT)
15.0 Distribution Center (GA_DIST_CENTER)
2.0 solutions within EPS*DIST.CENTER in bucket (GA_DIST_CENTER_EPS)
400000 Max nb. protein conformations in final bucket (GA_MAX_BUCKET_POP)
5.0 Local Residue lowest occupied energy cutoff (GA_RESIDUE_MIN_ENERGY_CUTOFF)
0.0 Occupied conformers in MIN_ENRG_CUTOFF are deleted (GA_OCCUPANCY_CUTOFF)
0.7 Pop. % for dE calculation (GA_DELTA_E)
-1 Disabled when -1 (GA_SPHERE_FOCUS_RESID)
20.0 Up to how many Angstorms to include residues (GA_SPHERE_PROBE_RADIUS)
0 GA output format: 0 display screen, 1 file (GA_OUTPUT)
###########PASCAL COMTE GENETIC ALGORITHM PARAMETERS FOR STEP 2################