BioBB AMBER Command Line Help
Generic usage:
biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>
Leap_solvate
Wrapper of the AmberTools (AMBER MD Package) leap tool module.
Get help
Command:
leap_solvate -h
usage: leap_solvate [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH [--input_lib_path INPUT_LIB_PATH] [--input_frcmod_path INPUT_FRCMOD_PATH] [--input_params_path INPUT_PARAMS_PATH] [--input_prep_path INPUT_PREP_PATH] [--input_source_path INPUT_SOURCE_PATH] --output_pdb_path OUTPUT_PDB_PATH --output_top_path OUTPUT_TOP_PATH --output_crd_path OUTPUT_CRD_PATH
Generating and solvating a system box for an AMBER MD system. using tLeap program from AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_pdb_path INPUT_PDB_PATH
Input 3D structure PDB file. Accepted formats: pdb.
--input_lib_path INPUT_LIB_PATH
Input ligand library parameters file. Accepted formats: lib, zip.
--input_frcmod_path INPUT_FRCMOD_PATH
Input ligand frcmod parameters file. Accepted formats: frcmod, zip.
--input_params_path INPUT_PARAMS_PATH
Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.
--input_prep_path INPUT_PREP_PATH
Additional leap parameter files to load with loadAmberPrep Leap command. Accepted formats: leapin, in, txt, zip.
--input_source_path INPUT_SOURCE_PATH
Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.
--output_pdb_path OUTPUT_PDB_PATH
Output 3D structure PDB file matching the topology file. Accepted formats: pdb.
--output_top_path OUTPUT_TOP_PATH
Output topology file (AMBER ParmTop). Accepted formats: top.
--output_crd_path OUTPUT_CRD_PATH
Output coordinates file (AMBER crd). Accepted formats: crd.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_pdb_path (string): Input 3D structure PDB file. File type: input. Sample file. Accepted formats: PDB
input_lib_path (string): Input ligand library parameters file. File type: input. Sample file. Accepted formats: LIB, ZIP
input_frcmod_path (string): Input ligand frcmod parameters file. File type: input. Sample file. Accepted formats: FRCMOD, ZIP
input_params_path (string): Additional leap parameter files to load with loadAmberParams Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
input_prep_path (string): Additional leap parameter files to load with loadAmberPrep Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
input_source_path (string): Additional leap command files to load with source Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
output_pdb_path (string): Output 3D structure PDB file matching the topology file. File type: output. Sample file. Accepted formats: PDB
output_top_path (string): Output topology file (AMBER ParmTop). File type: output. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
output_crd_path (string): Output coordinates file (AMBER crd). File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
forcefield (array): ([protein.ff14SB,DNA.bsc1,gaff]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. “/path/to/leaprc.protein.ff14SB” or “protein.ff14SB”). Default values: [”protein.ff14SB”,”DNA.bsc1”,”gaff”]..
water_type (string): (TIP3PBOX) Water molecule parameters to be used for the topology. .
box_type (string): (truncated_octahedron) Type for the MD system box. .
ions_type (string): (ionsjc_tip3p) Ions type. .
neutralise (boolean): (False) Energetically neutralise the system adding the necessary counterions..
iso (boolean): (False) Make the box isometric..
positive_ions_number (integer): (0) Number of additional positive ions to include in the system box..
negative_ions_number (integer): (0) Number of additional negative ions to include in the system box..
positive_ions_type (string): (Na+) Type of additional positive ions to include in the system box. .
negative_ions_type (string): (Cl-) Type of additional negative ions to include in the system box. .
distance_to_molecule (number): (8.0) Size for the MD system box -in Angstroms-, defined such as the minimum distance between any atom originally present in solute and the edge of the periodic box is given by this distance parameter..
closeness (number): (1.0) How close, in Å, solvent ATOMs may come to solute ATOMs..
binary_path (string): (tleap) Path to the tleap executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
box_type: truncated_octahedron
distance_to_molecule: '9.0'
forcefield:
- protein.ff14SB
remove_tmp: true
water_type: TIP3PBOX
Docker config file
properties:
box_type: truncated_octahedron
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
distance_to_molecule: '9.0'
forcefield:
- protein.ff14SB
water_type: TIP3PBOX
Command line
leap_solvate --config config_leap_solvate.yml --input_pdb_path structure.leap.pdb --input_lib_path ligand.lib --input_frcmod_path ligand.frcmod --input_params_path frcmod.ionsdang_spce.txt --input_prep_path heme_all.in --input_source_path leaprc.water.spce.txt --output_pdb_path structure.solv.pdb --output_top_path structure.solv.top --output_crd_path structure.solv.crd
JSON
Common config file
{
"properties": {
"forcefield": [
"protein.ff14SB"
],
"water_type": "TIP3PBOX",
"distance_to_molecule": "9.0",
"box_type": "truncated_octahedron",
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"forcefield": [
"protein.ff14SB"
],
"water_type": "TIP3PBOX",
"distance_to_molecule": "9.0",
"box_type": "truncated_octahedron",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
leap_solvate --config config_leap_solvate.json --input_pdb_path structure.leap.pdb --input_lib_path ligand.lib --input_frcmod_path ligand.frcmod --input_params_path frcmod.ionsdang_spce.txt --input_prep_path heme_all.in --input_source_path leaprc.water.spce.txt --output_pdb_path structure.solv.pdb --output_top_path structure.solv.top --output_crd_path structure.solv.crd
Sander_mdrun
Wrapper of the AmberTools (AMBER MD Package) sander tool module.
Get help
Command:
sander_mdrun -h
usage: sander_mdrun [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_crd_path INPUT_CRD_PATH [--input_mdin_path INPUT_MDIN_PATH] [--input_cpin_path INPUT_CPIN_PATH] [--input_ref_path INPUT_REF_PATH] --output_log_path OUTPUT_LOG_PATH --output_traj_path OUTPUT_TRAJ_PATH --output_rst_path OUTPUT_RST_PATH [--output_cpout_path OUTPUT_CPOUT_PATH] [--output_cprst_path OUTPUT_CPRST_PATH] [--output_mdinfo_path OUTPUT_MDINFO_PATH]
Running energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_mdin_path INPUT_MDIN_PATH
Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.
--input_cpin_path INPUT_CPIN_PATH
Input constant pH file (AMBER cpin). Accepted formats: cpin.
--input_ref_path INPUT_REF_PATH
Input reference coordinates for position restraints. Accepted formats: rst, rst7.
--output_cpout_path OUTPUT_CPOUT_PATH
Output constant pH file (AMBER cpout). Accepted formats: cpout.
--output_cprst_path OUTPUT_CPRST_PATH
Output constant pH restart file (AMBER rstout). Accepted formats: cprst.
--output_mdinfo_path OUTPUT_MDINFO_PATH
Output MD info. Accepted formats: mdinfo.
required arguments:
--input_top_path INPUT_TOP_PATH
Input topology file (AMBER ParmTop). Accepted formats: top, prmtop, parmtop.
--input_crd_path INPUT_CRD_PATH
Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd.
--output_log_path OUTPUT_LOG_PATH
Output log file. Accepted formats: log, out, txt.
--output_traj_path OUTPUT_TRAJ_PATH
Output trajectory file. Accepted formats: trj, crd, mdcrd, x.
--output_rst_path OUTPUT_RST_PATH
Output restart file. Accepted formats: rst, rst7.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Input topology file (AMBER ParmTop). File type: input. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
input_crd_path (string): Input coordinates file (AMBER crd). File type: input. Sample file. Accepted formats: CRD, MDCRD, INPCRD, NETCDF, NC, NCRST, RST
input_mdin_path (string): Input configuration file (MD run options) (AMBER mdin). File type: input. Sample file. Accepted formats: MDIN, IN, TXT
input_cpin_path (string): Input constant pH file (AMBER cpin). File type: input. Sample file. Accepted formats: CPIN
input_ref_path (string): Input reference coordinates for position restraints. File type: input. Sample file. Accepted formats: RST, RST7, NETCDF, NC, NCRST, CRD
output_log_path (string): Output log file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O
output_traj_path (string): Output trajectory file. File type: output. Sample file. Accepted formats: TRJ, CRD, MDCRD, X, NETCDF, NC
output_rst_path (string): Output restart file. File type: output. Sample file. Accepted formats: RST, RST7, NETCDF, NC, NCRST
output_cpout_path (string): Output constant pH file (AMBER cpout). File type: output. Sample file. Accepted formats: CPOUT
output_cprst_path (string): Output constant pH restart file (AMBER rstout). File type: output. Sample file. Accepted formats: CPRST, RST, RST7
output_mdinfo_path (string): Output MD info. File type: output. Sample file. Accepted formats: MDINFO
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
mdin (object): ({}) Sander MD run options specification. (Used if input_mdin_path is None).
simulation_type (string): (minimization) Default options for the mdin file. Each creates a different mdin file. .
binary_path (string): (sander) sander binary path to be used..
direct_mdin (boolean): (False) Use input_mdin_path as it is, skip file parsing..
mpi_bin (string): (None) Path to the MPI runner. Usually “mpirun” or “srun”..
mpi_np (integer): (0) Number of MPI processes. Usually an integer bigger than 1..
mpi_flags (string): (None) Path to the MPI hostlist file..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
mdin:
ioutfm: 0
maxcyc: 500
ntwx: 100
remove_tmp: true
simulation_type: minimization
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
mdin:
ioutfm: 0
maxcyc: 500
ntwx: 100
simulation_type: minimization
Command line
sander_mdrun --config config_sander_mdrun.yml --input_top_path cln025.prmtop --input_crd_path cln025.inpcrd --input_mdin_path npt.mdin --input_cpin_path cln025.cpin --input_ref_path sander.rst --output_log_path sander.log --output_traj_path sander.x --output_rst_path sander.rst --output_cpout_path sander.cpout --output_cprst_path sander.cprst --output_mdinfo_path sander.mdinfo
JSON
Common config file
{
"properties": {
"simulation_type": "minimization",
"mdin": {
"maxcyc": 500,
"ntwx": 100,
"ioutfm": 0
},
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"simulation_type": "minimization",
"mdin": {
"maxcyc": 500,
"ntwx": 100,
"ioutfm": 0
},
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
sander_mdrun --config config_sander_mdrun.json --input_top_path cln025.prmtop --input_crd_path cln025.inpcrd --input_mdin_path npt.mdin --input_cpin_path cln025.cpin --input_ref_path sander.rst --output_log_path sander.log --output_traj_path sander.x --output_rst_path sander.rst --output_cpout_path sander.cpout --output_cprst_path sander.cprst --output_mdinfo_path sander.mdinfo
Cestats_run
Wrapper of the AmberTools (AMBER MD Package) cestats tool module.
Get help
Command:
cestats_run -h
usage: cestats_run [-h] [--config CONFIG] --input_cein_path INPUT_CEIN_PATH --input_ceout_path INPUT_CEOUT_PATH --output_dat_path OUTPUT_DAT_PATH [--output_population_path OUTPUT_POPULATION_PATH] [--output_chunk_path OUTPUT_CHUNK_PATH] [--output_cumulative_path OUTPUT_CUMULATIVE_PATH] [--output_conditional_path OUTPUT_CONDITIONAL_PATH] [--output_chunk_conditional_path OUTPUT_CHUNK_CONDITIONAL_PATH]
Analyzing the results of constant Redox potential MD simulations using cestats tool from the AMBER MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_cein_path INPUT_CEIN_PATH
Input cein or cpein file (from pmemd or sander) with titrating residue information. Accepted formats: cein, cpein.
--input_ceout_path INPUT_CEOUT_PATH
Output ceout file (AMBER ceout). Accepted formats: ceout.
--output_dat_path OUTPUT_DAT_PATH
Output file to which the standard calceo-type statistics are written. Accepted formats: dat, out, txt, o.
--output_population_path OUTPUT_POPULATION_PATH
Output file where protonation state populations are printed for every state of every residue. Accepted formats: dat, out, txt, o.
--output_chunk_path OUTPUT_CHUNK_PATH
Output file where the time series data calculated over chunks of the simulation are printed. Accepted formats: dat, out, txt, o.
--output_cumulative_path OUTPUT_CUMULATIVE_PATH
Output file where the cumulative time series data is printed. Accepted formats: dat, out, txt, o.
--output_conditional_path OUTPUT_CONDITIONAL_PATH
Output file with requested conditional probabilities. Accepted formats: dat, out, txt, o.
--output_chunk_conditional_path OUTPUT_CHUNK_CONDITIONAL_PATH
Output file with a time series of the conditional probabilities over a trajectory split up into chunks. Accepted formats: dat, out, txt, o.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_cein_path (string): Input cein or cpein file (from pmemd or sander) with titrating residue information. File type: input. Sample file. Accepted formats: CEIN, CPEIN
input_ceout_path (string): Output ceout file (AMBER ceout). File type: input. Sample file. Accepted formats: CEOUT, ZIP, GZIP, GZ
output_dat_path (string): Output file to which the standard calceo-type statistics are written. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_population_path (string): Output file where protonation state populations are printed for every state of every residue. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_chunk_path (string): Output file where the time series data calculated over chunks of the simulation are printed. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_cumulative_path (string): Output file where the cumulative time series data is printed. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_conditional_path (string): Output file with requested conditional probabilities. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_chunk_conditional_path (string): Output file with a time series of the conditional probabilities over a trajectory split up into chunks. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
timestep (number): (0.002) Simulation time step -in ps-, used to print data as a function of time..
verbose (boolean): (False) Controls how much information is printed to the calceo-style output file. Options are: False - Just print fraction protonated. True - Print everything calceo prints..
interval (integer): (1000) Interval between which to print out time series data like chunks, cumulative data, and running averages. It is also used as the window of the conditional probability time series..
reduced (boolean): (True) Print out reduction fraction instead of oxidation fraction in time series data..
eos (boolean): (False) Print predicted Eos -via Nernst equation- in place of fraction reduced or oxidized..
calceo (boolean): (True) Triggers the calceo-style output..
running_avg_window (integer): (100) Defines a window size -in MD steps- for a moving, running average time series..
chunk_window (integer): (100) Computes the time series data over a chunk of the simulation of this specified size -window- time steps..
cumulative (boolean): (False) Computes the cumulative average time series data over the course of the trajectory..
fix_remd (string): () This option will trigger cestats to reassemble the titration data into pH-specific ensembles. This is an exclusive mode of the program, no other analyses will be done..
conditional (string): () Evaluates conditional probabilities. CONDITIONAL should be a string of the format:
: , : ,… or :PROT, :DEPROT,… or : ; , :PROT,… where is the residue number in the prmtop and is either the state number or -p-rotonated or -d-eprotonated, case-insensitive.. binary_path (string): (cestats) Path to the cestats executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
Command line
cestats_run --config config_cestats_run.yml --input_cein_path structure.cein --input_ceout_path sander.ceout.gz --output_dat_path cestats.dat --output_population_path cestats.dat --output_chunk_path cestats.dat --output_cumulative_path cestats.dat --output_conditional_path cestats.dat --output_chunk_conditional_path cestats.dat
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
cestats_run --config config_cestats_run.json --input_cein_path structure.cein --input_ceout_path sander.ceout.gz --output_dat_path cestats.dat --output_population_path cestats.dat --output_chunk_path cestats.dat --output_cumulative_path cestats.dat --output_conditional_path cestats.dat --output_chunk_conditional_path cestats.dat
Pmemd_mdrun
Wrapper of the AmberTools (AMBER MD Package) pmemd tool module.
Get help
Command:
pmemd_mdrun -h
usage: pmemd_mdrun [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_crd_path INPUT_CRD_PATH [--input_mdin_path INPUT_MDIN_PATH] [--input_cpin_path INPUT_CPIN_PATH] [--input_ref_path INPUT_REF_PATH] --output_log_path OUTPUT_LOG_PATH --output_traj_path OUTPUT_TRAJ_PATH --output_rst_path OUTPUT_RST_PATH [--output_cpout_path OUTPUT_CPOUT_PATH] [--output_cprst_path OUTPUT_CPRST_PATH] [--output_mdinfo_path OUTPUT_MDINFO_PATH]
Running molecular dynamics using pmemd tool from the AMBER MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Input topology file (AMBER ParmTop). Accepted formats: top, prmtop, parmtop.
--input_crd_path INPUT_CRD_PATH
Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd.
--input_mdin_path INPUT_MDIN_PATH
Input configuration file (MD run options) (AMBER mdin). Accepted formats: mdin, in, txt.
--input_cpin_path INPUT_CPIN_PATH
Input constant pH file (AMBER cpin). Accepted formats: cpin.
--input_ref_path INPUT_REF_PATH
Input reference coordinates for position restraints. Accepted formats: rst, rst7.
--output_log_path OUTPUT_LOG_PATH
Output log file. Accepted formats: log, out, txt.
--output_traj_path OUTPUT_TRAJ_PATH
Output trajectory file. Accepted formats: trj, crd, mdcrd, x.
--output_rst_path OUTPUT_RST_PATH
Output restart file. Accepted formats: rst, rst7.
--output_cpout_path OUTPUT_CPOUT_PATH
Output constant pH file (AMBER cpout). Accepted formats: cpout.
--output_cprst_path OUTPUT_CPRST_PATH
Output constant pH restart file (AMBER rstout). Accepted formats: cprst.
--output_mdinfo_path OUTPUT_MDINFO_PATH
Output MD info. Accepted formats: mdinfo.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Input topology file (AMBER ParmTop). File type: input. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
input_crd_path (string): Input coordinates file (AMBER crd). File type: input. Sample file. Accepted formats: CRD, MDCRD, INPCRD, RST, RST7, NETCDF, NC, NCRST
input_mdin_path (string): Input configuration file (MD run options) (AMBER mdin). File type: input. Sample file. Accepted formats: MDIN, IN, TXT
input_cpin_path (string): Input constant pH file (AMBER cpin). File type: input. Sample file. Accepted formats: CPIN
input_ref_path (string): Input reference coordinates for position restraints. File type: input. Sample file. Accepted formats: CRD, MDCRD, INPCRD, RST, RST7, NETCDF, NC, NCRST
output_log_path (string): Output log file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O
output_traj_path (string): Output trajectory file. File type: output. Sample file. Accepted formats: TRJ, CRD, MDCRD, X, NETCDF, NC
output_rst_path (string): Output restart file. File type: output. Sample file. Accepted formats: RST, RST7, NETCDF, NC, NCRST
output_cpout_path (string): Output constant pH file (AMBER cpout). File type: output. Sample file. Accepted formats: CPOUT
output_cprst_path (string): Output constant pH restart file (AMBER rstout). File type: output. Sample file. Accepted formats: CPRST, RST, RST7
output_mdinfo_path (string): Output MD info. File type: output. Sample file. Accepted formats: MDINFO
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
mdin (object): ({}) pmemd MD run options specification. (Used if input_mdin_path is None).
binary_path (string): (pmemd) pmemd binary path to be used..
simulation_type (string): (minimization) Default options for the mdin file. Each creates a different mdin file. .
mpi_bin (string): (None) Path to the MPI runner. Usually “mpirun” or “srun”..
mpi_np (integer): (0) Number of MPI processes. Usually an integer bigger than 1..
mpi_flags (string): (None) Path to the MPI hostlist file..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
YAML
Common config file
properties:
mdin:
ioutfm: 0
maxcyc: 500
ntwx: 100
remove_tmp: true
simulation_type: minimization
Command line
pmemd_mdrun --config config_pmemd_mdrun.yml --input_top_path cln025.prmtop --input_crd_path cln025.inpcrd --input_mdin_path npt.mdin --input_cpin_path cln025.cpin --input_ref_path sander.rst --output_log_path sander.log --output_traj_path sander.x --output_rst_path sander.rst --output_cpout_path sander.cpout --output_cprst_path sander.cprst --output_mdinfo_path sander.mdinfo
JSON
Common config file
{
"properties": {
"simulation_type": "minimization",
"mdin": {
"maxcyc": 500,
"ntwx": 100,
"ioutfm": 0
},
"remove_tmp": true
}
}
Command line
pmemd_mdrun --config config_pmemd_mdrun.json --input_top_path cln025.prmtop --input_crd_path cln025.inpcrd --input_mdin_path npt.mdin --input_cpin_path cln025.cpin --input_ref_path sander.rst --output_log_path sander.log --output_traj_path sander.x --output_rst_path sander.rst --output_cpout_path sander.cpout --output_cprst_path sander.cprst --output_mdinfo_path sander.mdinfo
Pdb4amber_run
Wrapper of the AmberTools (AMBER MD Package) pdb4amber tool module.
Get help
Command:
pdb4amber_run -h
usage: pdb4amber_run [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_pdb_path OUTPUT_PDB_PATH
Analyse PDB files and clean them for further usage, especially with the LEaP programs of Amber, using pdb4amber tool from the AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_pdb_path INPUT_PDB_PATH
Input 3D structure PDB file. Accepted formats: pdb.
--output_pdb_path OUTPUT_PDB_PATH
Output 3D structure PDB file. Accepted formats: pdb.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_pdb_path (string): Input 3D structure PDB file. File type: input. Sample file. Accepted formats: PDB
output_pdb_path (string): Output 3D structure PDB file. File type: output. Sample file. Accepted formats: PDB
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
remove_hydrogens (boolean): (False) Remove hydrogen atoms from the PDB file..
remove_waters (boolean): (False) Remove water molecules from the PDB file..
constant_pH (boolean): (False) Rename ionizable residues e.g. GLU,ASP,HIS for constant pH simulation..
reduce (boolean): (False) Run Reduce first to add hydrogen atoms..
binary_path (string): (pdb4amber) Path to the pdb4amber executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
Command line
pdb4amber_run --config config_pdb4amber_run.yml --input_pdb_path 1aki_fixed.pdb --output_pdb_path structure.pdb4amber.pdb
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
pdb4amber_run --config config_pdb4amber_run.json --input_pdb_path 1aki_fixed.pdb --output_pdb_path structure.pdb4amber.pdb
Process_mdout
Wrapper of the AmberTools (AMBER MD Package) process_mdout tool module.
Get help
Command:
process_mdout -h
usage: process_mdout [-h] [--config CONFIG] --input_log_path INPUT_LOG_PATH --output_dat_path OUTPUT_DAT_PATH
Parses the AMBER (sander) MD output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_log_path INPUT_LOG_PATH
AMBER (sander) MD output (log) file. Accepted formats: log, out, txt, o.
--output_dat_path OUTPUT_DAT_PATH
Dat output file containing data from the specified terms along the MD process. File type: output. Accepted formats: dat, txt, csv.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_log_path (string): AMBER (sander) MD output (log) file. File type: input. Sample file. Accepted formats: LOG, OUT, TXT, O
output_dat_path (string): Dat output file containing data from the specified terms along the minimization process. File type: output. Sample file. Accepted formats: DAT, TXT, CSV
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
terms (array): ([ETOT]) Statistics descriptors. .
binary_path (string): (process_mdout.perl) Path to the process_mdout.perl executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
terms:
- TEMP
- VOLUME
- EKTOT
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
terms:
- TEMP
- VOLUME
- EKTOT
Command line
process_mdout --config config_process_mdout.yml --input_log_path sander.heat.log --output_dat_path sander.md.temp.dat
JSON
Common config file
{
"properties": {
"terms": [
"TEMP",
"VOLUME",
"EKTOT"
],
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"terms": [
"TEMP",
"VOLUME",
"EKTOT"
],
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
process_mdout --config config_process_mdout.json --input_log_path sander.heat.log --output_dat_path sander.md.temp.dat
Leap_add_ions
Wrapper of the AmberTools (AMBER MD Package) leap tool module.
Get help
Command:
leap_add_ions -h
usage: leap_add_ions [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH [--input_lib_path INPUT_LIB_PATH] [--input_frcmod_path INPUT_FRCMOD_PATH] [--input_params_path INPUT_PARAMS_PATH] [--input_prep_path INPUT_PREP_PATH] [--input_source_path INPUT_SOURCE_PATH] --output_pdb_path OUTPUT_PDB_PATH --output_top_path OUTPUT_TOP_PATH --output_crd_path OUTPUT_CRD_PATH
Adds counterions to a system box for an AMBER MD system using tLeap.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_pdb_path INPUT_PDB_PATH
Input 3D structure PDB file. Accepted formats: pdb.
--input_lib_path INPUT_LIB_PATH
Input ligand library parameters file. Accepted formats: lib, zip.
--input_frcmod_path INPUT_FRCMOD_PATH
Input ligand frcmod parameters file. Accepted formats: frcmod, zip.
--input_params_path INPUT_PARAMS_PATH
Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.
--input_prep_path INPUT_PREP_PATH
Additional leap parameter files to load with loadAmberPrep Leap command. Accepted formats: leapin, in, txt, zip.
--input_source_path INPUT_SOURCE_PATH
Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.
--output_pdb_path OUTPUT_PDB_PATH
Output 3D structure PDB file matching the topology file. Accepted formats: pdb.
--output_top_path OUTPUT_TOP_PATH
Output topology file (AMBER ParmTop). Accepted formats: top.
--output_crd_path OUTPUT_CRD_PATH
Output coordinates file (AMBER crd). Accepted formats: crd.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_pdb_path (string): Input 3D structure PDB file. File type: input. Sample file. Accepted formats: PDB
input_lib_path (string): Input ligand library parameters file. File type: input. Sample file. Accepted formats: LIB, ZIP
input_frcmod_path (string): Input ligand frcmod parameters file. File type: input. Sample file. Accepted formats: FRCMOD, ZIP
input_params_path (string): Additional leap parameter files to load with loadAmberParams Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
input_prep_path (string): Additional leap parameter files to load with loadAmberPrep Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
input_source_path (string): Additional leap command files to load with source Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
output_pdb_path (string): Output 3D structure PDB file matching the topology file. File type: output. Sample file. Accepted formats: PDB
output_top_path (string): Output topology file (AMBER ParmTop). File type: output. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
output_crd_path (string): Output coordinates file (AMBER crd). File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
forcefield (array): ([protein.ff14SB,DNA.bsc1,gaff]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. “/path/to/leaprc.protein.ff14SB” or “protein.ff14SB”). Default values: [”protein.ff14SB”,”DNA.bsc1”,”gaff”]..
water_type (string): (TIP3PBOX) Water molecule parameters to be used for the topology. .
box_type (string): (truncated_octahedron) Type for the MD system box. .
ions_type (string): (ionsjc_tip3p) Ions type. .
neutralise (boolean): (True) Energetically neutralise the system adding the necessary counterions..
ionic_concentration (number): (50.0) Additional ionic concentration to include in the system box. Units in Mol/L..
positive_ions_number (integer): (0) Number of additional positive ions to include in the system box..
negative_ions_number (integer): (0) Number of additional negative ions to include in the system box..
positive_ions_type (string): (Na+) Type of additional positive ions to include in the system box. .
negative_ions_type (string): (Cl-) Type of additional negative ions to include in the system box. .
binary_path (string): (tleap) Path to the tleap executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
box_type: truncated_octahedron
forcefield:
- DNA.bsc1
ionic_concentration: 100
ions_type: ionsjc_tip4pew
positive_ions_type: K+
water_type: OPCBOX
Docker config file
properties:
box_type: truncated_octahedron
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
forcefield:
- DNA.bsc1
ionic_concentration: 100
ions_type: ionsjc_tip4pew
positive_ions_type: K+
water_type: OPCBOX
Command line
leap_add_ions --config config_leap_add_ions.yml --input_pdb_path structure.solv.pdb --input_lib_path ligand.lib --input_frcmod_path ligand.frcmod --input_params_path frcmod.ionsdang_spce.txt --input_prep_path frcmod.ionsdang_spce.txt --input_source_path leaprc.water.spce.txt --output_pdb_path structure.ions.pdb --output_top_path structure.ions.top --output_crd_path structure.ions.crd
JSON
Common config file
{
"properties": {
"forcefield": [
"DNA.bsc1"
],
"water_type": "OPCBOX",
"ions_type": "ionsjc_tip4pew",
"box_type": "truncated_octahedron",
"ionic_concentration": 100,
"positive_ions_type": "K+"
}
}
Docker config file
{
"properties": {
"forcefield": [
"DNA.bsc1"
],
"water_type": "OPCBOX",
"ions_type": "ionsjc_tip4pew",
"box_type": "truncated_octahedron",
"ionic_concentration": 100,
"positive_ions_type": "K+",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
leap_add_ions --config config_leap_add_ions.json --input_pdb_path structure.solv.pdb --input_lib_path ligand.lib --input_frcmod_path ligand.frcmod --input_params_path frcmod.ionsdang_spce.txt --input_prep_path frcmod.ionsdang_spce.txt --input_source_path leaprc.water.spce.txt --output_pdb_path structure.ions.pdb --output_top_path structure.ions.top --output_crd_path structure.ions.crd
Cphstats_run
Wrapper of the AmberTools (AMBER MD Package) cphstats tool module.
Get help
Command:
cphstats_run -h
usage: cphstats_run [-h] [--config CONFIG] --input_cpin_path INPUT_CPIN_PATH --input_cpout_path INPUT_CPOUT_PATH --output_dat_path OUTPUT_DAT_PATH [--output_population_path OUTPUT_POPULATION_PATH] [--output_chunk_path OUTPUT_CHUNK_PATH] [--output_cumulative_path OUTPUT_CUMULATIVE_PATH] [--output_conditional_path OUTPUT_CONDITIONAL_PATH] [--output_chunk_conditional_path OUTPUT_CHUNK_CONDITIONAL_PATH]
Analyzing the results of constant pH MD simulations using cphstats tool from the AMBER MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_cpin_path INPUT_CPIN_PATH
Input constant pH file (AMBER cpin). Accepted formats: cpin.
--input_cpout_path INPUT_CPOUT_PATH
Output constant pH file (AMBER cpout). Accepted formats: cpout.
--output_dat_path OUTPUT_DAT_PATH
Output file to which the standard calcpka-type statistics are written. Accepted formats: dat, out, txt, o.
--output_population_path OUTPUT_POPULATION_PATH
Output file where protonation state populations are printed for every state of every residue. Accepted formats: dat, out, txt, o.
--output_chunk_path OUTPUT_CHUNK_PATH
Output file where the time series data calculated over chunks of the simulation are printed. Accepted formats: dat, out, txt, o.
--output_cumulative_path OUTPUT_CUMULATIVE_PATH
Output file where the cumulative time series data is printed. Accepted formats: dat, out, txt, o.
--output_conditional_path OUTPUT_CONDITIONAL_PATH
Output file with requested conditional probabilities. Accepted formats: dat, out, txt, o.
--output_chunk_conditional_path OUTPUT_CHUNK_CONDITIONAL_PATH
Output file with a time series of the conditional probabilities over a trajectory split up into chunks. Accepted formats: dat, out, txt, o.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_cpin_path (string): Input constant pH file (AMBER cpin). File type: input. Sample file. Accepted formats: CPIN
input_cpout_path (string): Output constant pH file (AMBER cpout). File type: input. Sample file. Accepted formats: CPOUT, ZIP, GZIP
output_dat_path (string): Output file to which the standard calcpka-type statistics are written. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_population_path (string): Output file where protonation state populations are printed for every state of every residue. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_chunk_path (string): Output file where the time series data calculated over chunks of the simulation are printed. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_cumulative_path (string): Output file where the cumulative time series data is printed. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_conditional_path (string): Output file with requested conditional probabilities. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
output_chunk_conditional_path (string): Output file with a time series of the conditional probabilities over a trajectory split up into chunks. File type: output. Sample file. Accepted formats: DAT, OUT, TXT, O
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
timestep (number): (0.002) Simulation time step -in ps-, used to print data as a function of time..
verbose (boolean): (False) Controls how much information is printed to the calcpka-style output file. Options are: False - Just print fraction protonated. True - Print everything calcpka prints..
interval (integer): (1000) Interval between which to print out time series data like chunks, cumulative data, and running averages. It is also used as the window of the conditional probability time series..
protonated (boolean): (True) Print out protonation fraction instead of deprotonation fraction in time series data..
pka (boolean): (False) Print predicted pKas -via Henderson-Hasselbalch equation- in place of fraction -de-protonated..
calcpka (boolean): (True) Triggers the calcpka-style output..
running_avg_window (integer): (100) Defines a window size -in MD steps- for a moving, running average time series..
chunk_window (integer): (100) Computes the time series data over a chunk of the simulation of this specified size -window- time steps..
cumulative (boolean): (False) Computes the cumulative average time series data over the course of the trajectory..
fix_remd (string): () This option will trigger cphstats to reassemble the titration data into pH-specific ensembles. This is an exclusive mode of the program, no other analyses will be done..
conditional (string): () Evaluates conditional probabilities. CONDITIONAL should be a string of the format:
: , : ,… or :PROT, :DEPROT,… or : ; , :PROT,… where is the residue number in the prmtop and is either the state number or -p-rotonated or -d-eprotonated, case-insensitive.. binary_path (string): (cphstats) Path to the cphstats executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
Command line
cphstats_run --config config_cphstats_run.yml --input_cpin_path structure.cpin --input_cpout_path sander.pH.cpout --output_dat_path cphstats.pH.dat --output_population_path cphstats.pH.pop.dat --output_chunk_path cphstats.pH.dat --output_cumulative_path cphstats.pH.dat --output_conditional_path cphstats.pH.dat --output_chunk_conditional_path cphstats.pH.dat
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
cphstats_run --config config_cphstats_run.json --input_cpin_path structure.cpin --input_cpout_path sander.pH.cpout --output_dat_path cphstats.pH.dat --output_population_path cphstats.pH.pop.dat --output_chunk_path cphstats.pH.dat --output_cumulative_path cphstats.pH.dat --output_conditional_path cphstats.pH.dat --output_chunk_conditional_path cphstats.pH.dat
Process_minout
Wrapper of the AmberTools (AMBER MD Package) process_minout tool module.
Get help
Command:
process_minout -h
usage: process_minout [-h] [--config CONFIG] --input_log_path INPUT_LOG_PATH --output_dat_path OUTPUT_DAT_PATH
Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_log_path INPUT_LOG_PATH
AMBER (sander) minimization output (log) file. Accepted formats: log, out, txt, o.
--output_dat_path OUTPUT_DAT_PATH
Dat output file containing data from the specified terms along the minimization process. File type: output. Accepted formats: dat, txt, csv.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_log_path (string): AMBER (sander) Minimization output (log) file. File type: input. Sample file. Accepted formats: LOG, OUT, TXT, O
output_dat_path (string): Dat output file containing data from the specified terms along the minimization process. File type: output. Sample file. Accepted formats: DAT, TXT, CSV
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
terms (array): ([ENERGY]) Statistics descriptors. .
binary_path (string): (process_minout.perl) Path to the process_minout.perl executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
Command line
process_minout --config config_process_minout.yml --input_log_path sander.min.log --output_dat_path sander.min.energy.dat
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
process_minout --config config_process_minout.json --input_log_path sander.min.log --output_dat_path sander.min.energy.dat
Leap_build_linear_structure
Wrapper of the AmberTools (AMBER MD Package) leap tool module.
Get help
Command:
leap_build_linear_structure -h
usage: leap_build_linear_structure [-h] [--config CONFIG] --output_pdb_path OUTPUT_PDB_PATH
Building a linear (unfolded) 3D structure from an AA sequence.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--output_pdb_path OUTPUT_PDB_PATH
Linear (unfolded) 3D structure PDB file. Accepted formats: pdb.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
output_pdb_path (string): Linear (unfolded) 3D structure PDB file. File type: output. Sample file. Accepted formats: PDB
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
sequence (string): (ALA GLY SER PRO ARG ALA PRO GLY) Aminoacid sequence to convert to a linear 3D structure. Aminoacids should be written in 3-letter code, with a blank space between them..
forcefield (array): ([protein.ff14SB,DNA.bsc1,gaff]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. “/path/to/leaprc.protein.ff14SB” or “protein.ff14SB”). Default values: [”protein.ff14SB”,”DNA.bsc1”,”gaff”]..
build_library (boolean): (False) Generate AMBER lib file for the structure..
binary_path (string): (tleap) Path to the tleap executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
build_library: false
forcefield:
- protein.ff14SB
remove_tmp: true
sequence: ALA PRO SER ARG LYS ASP GLU GLY GLY ALA
Docker config file
properties:
build_library: false
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
forcefield:
- protein.ff14SB
sequence: ALA PRO SER ARG LYS ASP GLU GLY GLY ALA
Command line
leap_build_linear_structure --config config_leap_build_linear_structure.yml --output_pdb_path structure.pdb
JSON
Common config file
{
"properties": {
"sequence": "ALA PRO SER ARG LYS ASP GLU GLY GLY ALA",
"build_library": false,
"forcefield": [
"protein.ff14SB"
],
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"sequence": "ALA PRO SER ARG LYS ASP GLU GLY GLY ALA",
"build_library": false,
"forcefield": [
"protein.ff14SB"
],
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
leap_build_linear_structure --config config_leap_build_linear_structure.json --output_pdb_path structure.pdb
Nab_build_dna_structure
Wrapper of the AmberTools (AMBER MD Package) nab tool module.
Get help
Command:
nab_build_dna_structure -h
usage: nab_build_dna_structure [-h] [--config CONFIG] --output_pdb_path OUTPUT_PDB_PATH
Building a 3D structure from a DNA sequence using nab.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--output_pdb_path OUTPUT_PDB_PATH
Linear (unfolded) 3D structure PDB file. Accepted formats: pdb.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
output_pdb_path (string): DNA 3D structure PDB file. File type: output. Sample file. Accepted formats: PDB
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
sequence (string): (GCGCGGCTGATAAACGAAAGC) Nucleotide sequence to convert to a 3D structure. Nucleotides should be written in 1-letter code, with no spaces between them..
helix_type (string): (lbdna) DNA/RNA helix type. .
compiler (string): (gcc) Alternative C compiler for nab..
linker (string): (gfortran) Alternative Fortran linker for nab..
binary_path (string): (nab) Path to the nab executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
sequence: GCGCGGCTGATAAACGAAAGC
Command line
nab_build_dna_structure --config config_nab_build_dna_structure.yml --output_pdb_path ref_nab_build_dna_structure.pdb
JSON
Common config file
{
"properties": {
"sequence": "GCGCGGCTGATAAACGAAAGC",
"remove_tmp": true
}
}
Command line
nab_build_dna_structure --config config_nab_build_dna_structure.json --output_pdb_path ref_nab_build_dna_structure.pdb
Parmed_hmassrepartition
Wrapper of the AmberTools (AMBER MD Package) parmed tool module.
Get help
Command:
parmed_hmassrepartition -h
usage: parmed_hmassrepartition [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH [--output_top_path OUTPUT_TOP_PATH]
Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Input AMBER topology file. Accepted formats: top, parmtop, prmtop.
--output_top_path OUTPUT_TOP_PATH
Output topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Input AMBER topology file. File type: input. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
output_top_path (string): Output topology file (AMBER ParmTop). File type: output. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
binary_path (string): (parmed) Path to the parmed executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
Command line
parmed_hmassrepartition --config config_parmed_hmassrepartition.yml --input_top_path input.hmass.prmtop --output_top_path output.hmass.prmtop
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
parmed_hmassrepartition --config config_parmed_hmassrepartition.json --input_top_path input.hmass.prmtop --output_top_path output.hmass.prmtop
Cpptraj_randomize_ions
Wrapper of the AmberTools (AMBER MD Package) cpptraj tool module.
Get help
Command:
cpptraj_randomize_ions -h
usage: cpptraj_randomize_ions [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_crd_path INPUT_CRD_PATH --output_pdb_path OUTPUT_PDB_PATH --output_crd_path OUTPUT_CRD_PATH
Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Input topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.
--input_crd_path INPUT_CRD_PATH
Input coordinates file (AMBER crd). Accepted formats: crd, mdcrd, inpcrd.
--output_pdb_path OUTPUT_PDB_PATH
Structure PDB file with randomized ions. Accepted formats: pdb.
--output_crd_path OUTPUT_CRD_PATH
Structure CRD file with coordinates including randomized ions. Accepted formats: crd, mdcrd, inpcrd.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Input topology file (AMBER ParmTop). File type: input. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
input_crd_path (string): Input coordinates file (AMBER crd). File type: input. Sample file. Accepted formats: CRD, MDCRD, INPCRD
output_pdb_path (string): Structure PDB file with randomized ions. File type: output. Sample file. Accepted formats: PDB
output_crd_path (string): Structure CRD file with coordinates including randomized ions. File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
ion_mask (string): (:K+,Cl-,Na+) Ions to be randomized. Cpptraj mask syntax can be found at the official Cpptraj manual..
solute_mask (string): (:DA,DC,DG,DT,D?3,D?5) Solute (or set of atoms) around which the ions can get no closer than the distance specified. Cpptraj mask syntax can be found at the official Cpptraj manual..
distance (number): (5.0) Minimum distance cutoff for the ions around the defined solute..
overlap (number): (3.5) Minimum distance between ions..
binary_path (string): (cpptraj) Path to the cpptraj executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
Command line
cpptraj_randomize_ions --config config_cpptraj_randomize_ions.yml --input_top_path structure.ions.parmtop --input_crd_path structure.ions.crd --output_pdb_path structure.randIons.pdb --output_crd_path structure.randIons.crd
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_randomize_ions --config config_cpptraj_randomize_ions.json --input_top_path structure.ions.parmtop --input_crd_path structure.ions.crd --output_pdb_path structure.randIons.pdb --output_crd_path structure.randIons.crd
Amber_to_pdb
Wrapper of the AmberTools (AMBER MD Package) ambpdb tool module.
Get help
Command:
amber_to_pdb -h
usage: amber_to_pdb [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_crd_path INPUT_CRD_PATH --output_pdb_path OUTPUT_PDB_PATH
Generates a PDB structure from AMBER topology (parmtop) and coordinates (crd) files, using the ambpdb tool from the AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
AMBER topology file. Accepted formats: top, parmtop, prmtop.
--input_crd_path INPUT_CRD_PATH
AMBER coordinates file. Accepted formats: crd, mdcrd, inpcrd.
--output_pdb_path OUTPUT_PDB_PATH
Structure PDB file. Accepted formats: pdb.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): AMBER topology file. File type: input. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
input_crd_path (string): AMBER coordinates file. File type: input. Sample file. Accepted formats: CRD, MDCRD, INPCRD, RST
output_pdb_path (string): Structure PDB file. File type: output. Sample file. Accepted formats: PDB
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
binary_path (string): (ambpdb) Path to the ambpdb executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
Command line
amber_to_pdb --config config_amber_to_pdb.yml --input_top_path structure.leap.top --input_crd_path structure.leap.crd --output_pdb_path structure.ambpdb.pdb
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
amber_to_pdb --config config_amber_to_pdb.json --input_top_path structure.leap.top --input_crd_path structure.leap.crd --output_pdb_path structure.ambpdb.pdb
Leap_gen_top
Wrapper of the AmberTools (AMBER MD Package) leap tool module.
Get help
Command:
leap_gen_top -h
usage: leap_gen_top [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH [--input_lib_path INPUT_LIB_PATH] [--input_frcmod_path INPUT_FRCMOD_PATH] [--input_params_path INPUT_PARAMS_PATH] [--input_prep_path INPUT_PREP_PATH] [--input_source_path INPUT_SOURCE_PATH] --output_pdb_path OUTPUT_PDB_PATH --output_top_path OUTPUT_TOP_PATH --output_crd_path OUTPUT_CRD_PATH
Generating a MD topology from a molecule structure using tLeap program from AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_pdb_path INPUT_PDB_PATH
Input 3D structure PDB file. Accepted formats: pdb.
--input_lib_path INPUT_LIB_PATH
Input ligand library parameters file. Accepted formats: lib, zip.
--input_frcmod_path INPUT_FRCMOD_PATH
Input ligand frcmod parameters file. Accepted formats: frcmod, zip.
--input_params_path INPUT_PARAMS_PATH
Additional leap parameter files to load with loadAmberParams Leap command. Accepted formats: leapin, in, txt, zip.
--input_prep_path INPUT_PREP_PATH
Additional leap parameter files to load with loadAmberPrep Leap command. Accepted formats: leapin, in, txt, zip.
--input_source_path INPUT_SOURCE_PATH
Additional leap command files to load with source Leap command. Accepted formats: leapin, in, txt, zip.
--output_pdb_path OUTPUT_PDB_PATH
Output 3D structure PDB file matching the topology file. Accepted formats: pdb.
--output_top_path OUTPUT_TOP_PATH
Output topology file (AMBER ParmTop). Accepted formats: top.
--output_crd_path OUTPUT_CRD_PATH
Output coordinates file (AMBER crd). Accepted formats: crd.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_pdb_path (string): Input 3D structure PDB file. File type: input. Sample file. Accepted formats: PDB
input_lib_path (string): Input ligand library parameters file. File type: input. Sample file. Accepted formats: LIB, ZIP
input_frcmod_path (string): Input ligand frcmod parameters file. File type: input. Sample file. Accepted formats: FRCMOD, ZIP
input_params_path (string): Additional leap parameter files to load with loadAmberParams Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
input_prep_path (string): Additional leap parameter files to load with loadAmberPrep Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
input_source_path (string): Additional leap command files to load with source Leap command. File type: input. Sample file. Accepted formats: IN, LEAPIN, TXT, ZIP
output_pdb_path (string): Output 3D structure PDB file matching the topology file. File type: output. Sample file. Accepted formats: PDB
output_top_path (string): Output topology file (AMBER ParmTop). File type: output. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
output_crd_path (string): Output coordinates file (AMBER crd). File type: output. Sample file. Accepted formats: CRD, MDCRD, INPCRD
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
forcefield (array): ([protein.ff14SB,DNA.bsc1,gaff]) Forcefields to be used for the structure generation. Each item should be either a path to a leaprc file or a string with the leaprc file name if the force field is included with Amber (e.g. “/path/to/leaprc.protein.ff14SB” or “protein.ff14SB”). Default values: [”protein.ff14SB”,”DNA.bsc1”,”gaff”]..
binary_path (string): (tleap) Path to the tleap executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
forcefield:
- protein.ff14SB
remove_tmp: true
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
forcefield:
- protein.ff14SB
Command line
leap_gen_top --config config_leap_gen_top.yml --input_pdb_path structure.leapin.pdb --input_lib_path ligand.lib --input_frcmod_path ligand.frcmod --input_params_path frcmod.ionsdang_spce.txt --input_prep_path heme_all.in --input_source_path leaprc.water.spce.txt --output_pdb_path structure.leap.pdb --output_top_path structure.leap.top --output_crd_path structure.leap.crd
JSON
Common config file
{
"properties": {
"forcefield": [
"protein.ff14SB"
],
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"forcefield": [
"protein.ff14SB"
],
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
leap_gen_top --config config_leap_gen_top.json --input_pdb_path structure.leapin.pdb --input_lib_path ligand.lib --input_frcmod_path ligand.frcmod --input_params_path frcmod.ionsdang_spce.txt --input_prep_path heme_all.in --input_source_path leaprc.water.spce.txt --output_pdb_path structure.leap.pdb --output_top_path structure.leap.top --output_crd_path structure.leap.crd
Parmed_cpinutil
Wrapper of the AmberTools (AMBER MD Package) parmed tool module.
Get help
Command:
parmed_cpinutil -h
usage: parmed_cpinutil [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --output_cpin_path OUTPUT_CPIN_PATH [--output_top_path OUTPUT_TOP_PATH]
create a cpin file for constant pH simulations from an AMBER topology file using parmed program from AmberTools MD package.
options:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Input AMBER topology file. Accepted formats: top, parmtop, prmtop.
--output_cpin_path OUTPUT_CPIN_PATH
Output AMBER constant pH input (CPin) file. Accepted formats: cpin.
--output_top_path OUTPUT_TOP_PATH
Output topology file (AMBER ParmTop). Accepted formats: top, parmtop, prmtop.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Input AMBER topology file. File type: input. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
output_cpin_path (string): Output AMBER constant pH input (CPin) file. File type: output. Sample file. Accepted formats: CPIN
output_top_path (string): Output topology file (AMBER ParmTop). File type: output. Sample file. Accepted formats: TOP, PARMTOP, PRMTOP
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
resnames (string): (None) Residue names to include in CPIN file. .
igb (integer): (2) Generalized Born model which you intend to use to evaluate dynamics or protonation state swaps. .
system (string): (Unknown) Name of system to titrate..
binary_path (string): (cpinutil.py) Path to the cpinutil.py executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..
container_path (string): (None) Container path definition..
container_image (string): (afandiadib/ambertools:serial) Container image definition..
container_volume_path (string): (/tmp) Container volume path definition..
container_working_dir (string): (None) Container working directory definition..
container_user_id (string): (None) Container user_id definition..
container_shell_path (string): (/bin/bash) Path to default shell inside the container..
YAML
Common config file
properties:
igb: 2
remove_tmp: true
resnames: AS4 GL4
system: cln025
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
igb: 2
resnames: AS4 GL4
system: cln025
Command line
parmed_cpinutil --config config_parmed_cpinutil.yml --input_top_path structure.solv.top --output_cpin_path cln025.cpin --output_top_path cln025.cpH.prmtop
JSON
Common config file
{
"properties": {
"igb": 2,
"resnames": "AS4 GL4",
"system": "cln025",
"remove_tmp": true
}
}
Docker config file
{
"properties": {
"igb": 2,
"resnames": "AS4 GL4",
"system": "cln025",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Command line
parmed_cpinutil --config config_parmed_cpinutil.json --input_top_path structure.solv.top --output_cpin_path cln025.cpin --output_top_path cln025.cpH.prmtop