-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathsimu_config_implicit_solvent.yaml
executable file
·229 lines (200 loc) · 12.9 KB
/
simu_config_implicit_solvent.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
# Note: In addition to 'Yes' or 'No', all the other non-numerical values are treated as strings by YAML, quotes('') are placed somewhere to be sure.
# Compute platform info: device, OS, procssing platform, CUDA_precision
device : local # local or cluster
operating_system: macos # macos or linux or WSL. Not supporting pure Windows OS (due to NUPACK)
platform : CPU # CPU or CUDA or OpenCL
CUDA_precision: # single or double or mixed. only meaningful if CUDA or OpenCL
# Work directory and automate output directory "run{--run_num}". If not exist, will be automatically created
workdir: <path to your work directory>
# MMB-related paths: if not using MMB, just leave the value parts blank
mmb_dir: <path to MMB lib> # path to MMB dylib, something like "./Installer*/lib"
mmb : <path to MMB executable> # path to the MMB executable, something like "./Installer*/bin/MMB*"
# Control
quick_check_mode: 'No' # 'Yes' or 'No'. Yes': To run a certain mode for quick check.
# Will overwrite "Pipeline modules" settings with simplistic default values (seen below at the bottom)
# Output directory: {workdir}/run{run_num}
run_num: 1
# Pipeline mode:
mode: 'free aptamer'
# '2d structure': NUPACK
# '3d coarse': NUPACK + MMB
# '3d smooth': NUPACK + MMB + short MD relaxation (smoothing)
# 'coarse dock': NUPACK + MMB + docking
# 'smooth dock': NUPACK + MMB + short MD relaxation + docking
# 'free aptamer': NUPACK + MMB + MD sampling (aptamer)
# 'full dock': NUPACK + MMB + MD sampling (aptamer) + docking
# 'full binding': NUPACK + MMB + MD sampling (aptamer) + docking + MD sampling (aptamer-ligand complex)
# # `skip_MMB` can be used to skip MMB and NUPACK together, but no effecct if mode is '2d structure'.
# Information on DNA aptamer and target ligand if applicable
# 5'->3' DNA sequence
aptamer_seq: 'CCTGGGGGAGTATTGCGGAGGAAGG'
ligand:
ligand_type:
ligand_seq:
# `ligand` : pdb file name
# `ligand_type`: peptide, DNA, RNA, or other
# `ligand_seq` : ligand sequence if peptide, DNA, or RNA
# If not applicable for any of those 3 args (eg, no ligand), leave as blank => will become Python None
# mode, aptamer_seq and ligand: expect them to be specified in cmd line because they are likely to be more frequently changed
# Example provided in examples/:
example_target_pdb: 'examples/example_peptide_ligand.pdb' # an example of ligand: a peptide, used to test docking.
example_peptide_seq: 'YQTQTNSPRRAR'
# =========================== Pipeline modules: NUPACK and MMB ===========================
skip_MMB: 'No' # 'Yes' or 'No'.
# 'Yes': skip NUPACK and MMB together, directly proceed to MD sampling or dock (in "coarse dock")
# If MMB is not run because we are about to resume MD sampling, keep skip_MMB as 'No'
# NUPACK
secondary_structure_engine: NUPACK
ensemble: nostacking # nostacking or stacking; historical options in NUPACK3: none-nupack3, some-nupack3, all-nupack3
N_2D_structures: 1 # Number of predicted secondary structures
Mg_conc: 0.005 # Magnesium concentration used in NUPACK. [0, 0.2M]
# MMB
# No need to change the following 4 paths. Be sure to download `lib/mmb` folder from the E2EDNA GitHub repo
mmb_params : 'lib/mmb/parameters.csv' # parameter for the MMB executable
mmb_normal_template: 'lib/mmb/commands.template.dat' # MMB folding protocol template No.1
mmb_quick_template : 'lib/mmb/commands.template_quick.dat' # MMB folding protocol template No.2
mmb_slow_template : 'lib/mmb/commands.template_long.dat' # MMB folding protocol template No.3
fold_fidelity: 0.9 # MMB: if folding fidelity < this value, refold; unless the fold speed is 'quick'
fold_speed: quick # quick, normal, slow
# If skip_MMB is 'Yes', provide pdb filename of initial structure; otherwise, leave it blank
# init_structure: ./examples/foldedAptamer_0.pdb
init_structure:
# =========================== Pipeline module: OpenMM ===========================
# OpenMM
# # Whether to resume a simulation: if to resume, only applied to explicit solvent run; because implicit solvent run is fast
pickup: 'No' # 'Yes' or 'No'
# If `pickup` is 'Yes': only one of the `pickup_from_...` is 'Yes'. It makes no sense to resume both free aptamer and aptamer-ligand dynamics
pickup_from_freeAptamerChk: 'No' # 'Yes' or 'No'. 'Yes': resume a MD of free aptamer. Skip everything before.
pickup_from_complexChk : 'No' # 'Yes' or 'No'. 'Yes': resume a MD of aptamer-ligand. Skip everything before.
# If `pickup` is 'Yes':
# (1) must provide a checkpoint file (path/filename.chk): it will be copied to run{--run_num}
# .chk file contains data that is highly specific to the Context from which it was created, including OpenMM version.
# if checkpoint file is created on CUDA, does not work on CPU.
chk_file:
# (2) must provide topology file (path/filename.pdb): it will be copied to run{--run_num}
pickup_pdb:
# # If `pickup` is 'No': leave those 2 args above blank.
# # Environmental parameters of the simulation system
pressure: 1.0 # atm
temperature: 298.15 # Kevin: used to predict secondary structure and for MD thermostat
ionicStrength: 0.150 # Sodium concentration used by NUPACK and OpenMM. [Na] in [50M, 1100M] for NUPACK. Could be used in implicit solvent as well.
pH: 7.4 # Used to decide protonation states of aptamer and/or target ligand in OpenMM explicit waterbox
# # MD sampling: time and Langevin integrator
auto_sampling : 'No' # 'Yes' or 'No'. 'Yes': run sampling till reaction coordinate is converged. Currently only feasible in free aptamer sampling
autoMD_convergence_cutoff: 1.0e-2 # how small should average of PCA slopes be to count as 'converged'
max_aptamer_sampling_iter: 20 # number of allowable iterations before giving up on auto-sampling free aptamer - total max simulation length this * sampling_time
max_walltime: 24.0 # hours
skip_smoothing: 'Yes' # 'Yes' or 'No'. 'Yes': no short MD relaxation before MD sampling. Will be changed to 'No' if mode involves MD relaxation (3d smooth, smooth dock)
equilibration_time: 0.0005
smoothing_time:
aptamer_sampling_time: 0.001
complex_sampling_time:
time_step: 2.0
print_step: 0.05
# # The meanings of 6 arguments about MD time:
# ns. Initial equilibration time in nanoseconds
# ns. MD relax after getting the initial 3D structure from user or MMB before MD sampling. Set as Python None because no smoothing by default
# ns. Free aptamer sampling time in nanoseconds
# ns. Only required if running aptamer-ligand complex dynamics, ie, mode: 'full binding' or pickup_from_complexChk
# fs. MD time_step in fs
# ps. MD printout step in ps. ns > ps > fs
# # Create simulation system
# For more check out: http://docs.openmm.org/latest/userguide/application/02_running_sims.html#force-fields
# The force field is specified in __init__ of interfaces.py
force_field: amber14-all # amber14/protein.ff14SB, amber14/DNA.OL15, amber14/RNA.OL3, amber14/lipid17, etc.
hydrogen_mass: 1.5 # amu. Heavier hydrogen allows us to sample for longer time
# This applies only to hydrogens that are bonded to heavy atoms,
# and any mass added to the hydrogen is subtracted from the heavy atom.
# This keeps their total mass constant while slowing down the fast motions of hydrogens
# # Default is to use explicit solvent
water_model: amber14/tip3p # amber14/tip3p, amber14/tip3pfb, amber14/tip4pew, amber14/spce, 'no standalone water model', etc; Not used if implicit solvent
box_offset: 1.0 # nanometers
constraints: HBonds # HBonds, AllBonds, HAngles, None (Python string)
constraint_tolerance: 1.0e-6 # constraintTolerance of integrator
rigid_water: 'Yes' # 'Yes' or 'No'.
# Regardless of "constraints", OpenMM makes water molecules completely rigid, constraining both their bond lengths and angles;
# But by default OpenMM makes AMOEBA water flexible. If 'No', better to reduce integration step size to 0.5 fs
nonbonded_method: PME # Ewald, PME, LJPME, CutoffPeriodic, CutoffNonPeriodic, NoCutoff (Python string)
# Particle Mesh Ewald: efficient full electrostatics method in periodic boundary conditions to calculate long-range interactions
nonbonded_cutoff: 1.0 # nanometers
ewald_error_tolerance: 5.0e-4 # The error tolerance to use if nonbondedMethod is Ewald, PME, or LJPME.
friction: 1.0 # Langevin friction coefficient. Unit: 1/ps. Determines how strongly the system is coupled to the heat bath
# # Implicit solvent
implicit_solvent : 'Yes' # 'Yes' or 'No'. If 'No', can leave `implicit_solvent_model` as blank to become Python None
implicit_solvent_model: HCT # Amber GB: HCT, OBC1, OBC2, GBn, GBn2
soluteDielectric : 1.0 # 1.0 means no screening effect
solventDielectric: 78.5 # 78.5 for water
implicit_solvent_Kappa: # Debye screening parameter. Default is None. If specified, OpenMM will ignore params['implicit_solvent_salt_conc'] which is equal to params['ionicStrength']
# Kappa=1/Debye_length and can be computed using ionic strength and dielectrics of solute and solvent
leap_template: leap_template.in # leap_template.in: a functonal script is provided in E2EDNA package
DNA_force_field: DNA.OL15 # DNA.OL15 or DNA.bsc1. For free aptamer MD sampling, available from ambertools21
# For complex MD sampling: if target is peptide or RNA, will add "leaprc.protein.ff14SB" or "source leaprc.RNA.OL3" to leap input file.
# # !!!!
# # If `implicit_solvent`='Yes', uncomment out the following 2 args about nonbonded method to overwrite the earlier ones
nonbonded_method: CutoffNonPeriodic # CutoffPeriodic, CutoffNonPeriodic or NoCutoff
nonbonded_cutoff: 2.0 # nanometers. In implicit solvent models, better to pick a larger value such as 2.0 (OpenMM)
# # No periodic boundaries in implicit solvent system => nonbonded_method cannot be Ewald, PME, or LJPME => ewald_error_tolerance is not used even specified
# # PBC is used to avoid surface effects in explicit solvent and implicit solvent does not have solvent boundaries (the continuum goes on forever).
# =========================== Pipeline module: Lightdock ===========================
# Docking
docking_steps: 5 # number of steps for docking simulations
N_docked_structures: 1 # 2 # number of docked structures to output from the docker. If running binding, it will go this time (at linear cost) # TODO: "it will go this time"?
# =========================== Miscellaneous ===========================
# Pipeline parameters used in quick_check_mode:
#
# # NUPACk and MMB
# params['skip_MMB'] = False
# params['secondary_structure_engine'] = 'NUPACK'
# params['N_2D_structures'] = 1
# params['Mg_conc'] = 0.005
# params['fold_fidelity'] = 0.9
# params['fold_speed'] = 'quick'
# params['init_structure'] = None
#
# # OpenMM
# params['pickup'] = False
# params['pickup_from_freeAptamerChk'] = False
# params['pickup_from_complexChk'] = False
# params['chk_file'] = None
# params['pickup_pdb'] = None
#
# params['auto_sampling'] = False
# params['autoMD_convergence_cutoff'] = 1e-2 # not used if auto_sampling=False
# params['max_aptamer_sampling_iter'] = 2 # not used if auto_sampling=False
#
# params['equilibration_time'] = 0.0001 # ns. 50 steps
#
# if params['mode'] in ['3d smooth', 'smooth dock']:
# params['skip_smoothing'] = False
# params['smoothing_time'] = 0.001 # ns. 500 steps
# else:
# params['skip_smoothing'] = True
# params['smoothing_time'] = None
#
# params['aptamer_sampling_time'] = 0.002 # ns. 1000 steps
# if params['mode'] == 'full binding':
# params['complex_sampling_time'] = 0.002 # ns. 1000 steps
# params['time_step'] = 2.0 # fs
# params['print_step'] = 0.05 # ps. print out every 25 steps
# params['force_field'] = 'amber14-all'
# params['hydrogen_mass'] = 1.5
# params['water_model'] = 'amber14/tip3p'
# params['box_offset'] = 1.0
# params['constraints'] = 'HBonds'
# params['constraint_tolerance'] = 1.0e-6
# params['rigid_water'] = True
# params['nonbonded_method'] = 'PME'
# params['nonbonded_cutoff'] = 1.0
# params['ewald_error_tolerance'] = 5.0e-4
# params['friction'] = 1.0
# params['implicit_solvent'] = False
# params['implicit_solvent_model'] = None
# params['soluteDielectric'] = None
# params['solventDielectric'] = None
# params['implicit_solvent_Kappa'] = None
# params['leap_template'] = None
# params['DNA_force_field'] = None
#
# # LightDock
# params['docking_steps'] = 10
# params['N_docked_structures'] = 1