BioBB ANALYSIS Command Line Help
Generic usage:
biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>
Cpptraj_slice
Wrapper of the Ambertools Cpptraj module for extracting a particular trajectory slice from a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_slice -h
usage: cpptraj_slice [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Extracts a particular trajectory slice from a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed trajectory.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing..
end (integer): (-1) Ending frame for slicing..
steps (integer): (1) Step for slicing..
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
end: 20
format: netcdf
mask: c-alpha
start: 2
steps: 2
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: 20
format: netcdf
mask: c-alpha
start: 2
steps: 2
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: 20
format: netcdf
mask: c-alpha
start: 2
steps: 2
Command line
cpptraj_slice --config config_cpptraj_slice.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.slice.netcdf
JSON
Common config file
{
"properties": {
"start": 2,
"end": 20,
"steps": 2,
"mask": "c-alpha",
"format": "netcdf"
}
}
Docker config file
{
"properties": {
"start": 2,
"end": 20,
"steps": 2,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 2,
"end": 20,
"steps": 2,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_slice --config config_cpptraj_slice.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.slice.netcdf
Cpptraj_convert
Wrapper of the Ambertools Cpptraj module for converting between cpptraj compatible trajectory file formats and/or extracting a selection of atoms or frames.
Get help
Command:
cpptraj_convert -h
usage: cpptraj_convert [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Converts between cpptraj compatible trajectory file formats and/or extracts a selection of atoms or frames.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed structure.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing.
end (integer): (-1) Ending frame for slicing.
steps (integer): (1) Step for slicing.
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Command line
cpptraj_convert --config config_cpptraj_convert.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.convert.netcdf
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf"
}
}
Docker config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_convert --config config_cpptraj_convert.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.convert.netcdf
Cpptraj_dry
Wrapper of the Ambertools Cpptraj module for dehydrating a given cpptraj compatible trajectory stripping out solvent molecules and ions.
Get help
Command:
cpptraj_dry -h
usage: cpptraj_dry [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Dehydrates a given cpptraj compatible trajectory stripping out solvent molecules and ions.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed trajectory.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing..
end (integer): (-1) Ending frame for slicing..
steps (integer): (1) Step for slicing..
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Command line
cpptraj_dry --config config_cpptraj_dry.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.dry.netcdf
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf"
}
}
Docker config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_dry --config config_cpptraj_dry.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.dry.netcdf
Cpptraj_rmsf
Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_rmsf -h
usage: cpptraj_rmsf [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Calculates the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_exp_path INPUT_EXP_PATH
Path to the experimental reference file (required if reference = experimental).
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed analysis.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
input_exp_path (string): Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: PDB
output_cpptraj_path (string): Path to the output processed analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing.
end (integer): (-1) Ending frame for slicing.
steps (integer): (1) Step for slicing.
mask (string): (all-atoms) Mask definition. .
reference (string): (first) Reference definition. .
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:
end: -1
mask: c-alpha
reference: first
start: 1
steps: 1
Command line
cpptraj_rmsf --config config_cpptraj_rmsf.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rmsf.first.dat
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"reference": "first"
}
}
Command line
cpptraj_rmsf --config config_cpptraj_rmsf.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rmsf.first.dat
Gmx_trjconv_trj
Wrapper of the GROMACS trjconv module for converting between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.
Get help
Command:
gmx_trjconv_trj -h
usage: gmx_trjconv_trj [-h] [--config CONFIG] --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] [--input_top_path INPUT_TOP_PATH] --output_traj_path OUTPUT_TRAJ_PATH
Converts between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_index_path INPUT_INDEX_PATH
Path to the GROMACS index file. Accepted formats: ndx.
--input_top_path INPUT_TOP_PATH
Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
required arguments:
--input_traj_path INPUT_TRAJ_PATH
Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
--output_traj_path OUTPUT_TRAJ_PATH
Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_traj_path (string): Path to the output file. File type: output. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .
start (integer): (0) Time of first frame to read from trajectory (default unit ps)..
end (integer): (0) Time of last frame to read from trajectory (default unit ps)..
dt (integer): (0) Only write frame when t MOD dt = first time (ps)..
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
dt: 0
end: 0
selection: System
start: 0
Docker config file
properties:
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
dt: 0
end: 0
selection: System
start: 0
Singularity config file
properties:
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
dt: 0
end: 0
selection: System
start: 0
Command line
gmx_trjconv_trj --config config_gmx_trjconv_trj.yml --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_trjconv.trj.xtc
JSON
Common config file
{
"properties": {
"selection": "System",
"start": 0,
"end": 0,
"dt": 0
}
}
Docker config file
{
"properties": {
"selection": "System",
"start": 0,
"end": 0,
"dt": 0,
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"selection": "System",
"start": 0,
"end": 0,
"dt": 0,
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_trjconv_trj --config config_gmx_trjconv_trj.json --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_trjconv.trj.xtc
Cpptraj_mask
Wrapper of the Ambertools Cpptraj module for extracting a selection of atoms from a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_mask -h
usage: cpptraj_mask [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Extracts a selection of atoms from a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed trajectory.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing..
end (integer): (-1) Ending frame for slicing..
steps (integer): (1) Step for slicing..
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Command line
cpptraj_mask --config config_cpptraj_mask.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.mask.netcdf
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf"
}
}
Docker config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_mask --config config_cpptraj_mask.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.mask.netcdf
Cpptraj_rms
Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_rms -h
usage: cpptraj_rms [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] --output_cpptraj_path OUTPUT_CPPTRAJ_PATH [--output_traj_path OUTPUT_TRAJ_PATH]
Calculates the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_exp_path INPUT_EXP_PATH
Path to the experimental reference file (required if reference = experimental).
--output_traj_path OUTPUT_TRAJ_PATH
Path to the output processed trajectory.
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed analysis.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
input_exp_path (string): Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: PDB
output_cpptraj_path (string): Path to the output processed analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU
output_traj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing.
end (integer): (-1) Ending frame for slicing.
steps (integer): (1) Step for slicing.
mask (string): (all-atoms) Mask definition. .
reference (string): (first) Reference definition. .
nofit (boolean): (False) Do not perform best-fit RMSD.
norotate (boolean): (False) Translate but do not rotate coordinates.
nomod (boolean): (False) Do not modify coordinates.
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:
end: -1
mask: c-alpha
reference: first
start: 1
steps: 1
Command line
cpptraj_rms --config config_cpptraj_rms.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rms.first.dat --output_traj_path cpptraj.traj.dcd
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"reference": "first"
}
}
Command line
cpptraj_rms --config config_cpptraj_rms.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rms.first.dat --output_traj_path cpptraj.traj.dcd
Cpptraj_bfactor
Wrapper of the Ambertools Cpptraj module for calculating the Bfactor fluctuations of a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_bfactor -h
usage: cpptraj_bfactor [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Calculates the Bfactor fluctuations of a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_exp_path INPUT_EXP_PATH
Path to the experimental reference file (required if reference = experimental).
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed analysis.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
input_exp_path (string): Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: PDB
output_cpptraj_path (string): Path to the output processed analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing.
end (integer): (-1) Ending frame for slicing.
steps (integer): (1) Step for slicing.
mask (string): (all-atoms) Mask definition. .
reference (string): (first) Reference definition. .
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:
end: -1
mask: c-alpha
reference: first
start: 1
steps: 1
Command line
cpptraj_bfactor --config config_cpptraj_bfactor.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.bfactor.first.dat
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"reference": "first"
}
}
Command line
cpptraj_bfactor --config config_cpptraj_bfactor.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.bfactor.first.dat
Gmx_image
Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.
Get help
Command:
gmx_image -h
usage: gmx_image [-h] [--config CONFIG] --input_traj_path INPUT_TRAJ_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] --output_traj_path OUTPUT_TRAJ_PATH
Corrects periodicity (image) from a given GROMACS compatible trajectory file.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_index_path INPUT_INDEX_PATH
Path to the GROMACS index file. Accepted formats: ndx.
required arguments:
--input_traj_path INPUT_TRAJ_PATH
Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
--input_top_path INPUT_TOP_PATH
Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
--output_traj_path OUTPUT_TRAJ_PATH
Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_traj_path (string): Path to the output file. File type: output. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
fit_selection (string): (System) Group where the fitting will be performed. If input_index_path provided, check the file for the accepted values. .
center_selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .
cluster_selection (string): (System) Group assigned to be the cluster, onto which all atoms are wrapped around the box, such that they are closest to the center of mass of the cluster, which is iteratively updated. If input_index_path provided, check the file for the accepted values. .
output_selection (string): (System) Group that is going to be written in the output trajectory. If input_index_path provided, check the file for the accepted values. .
pbc (string): (mol) PBC treatment (see help text for full description) . .
center (boolean): (True) Center atoms in box..
ur (string): (compact) Unit-cell representation. .
fit (string): (none) Fit molecule to ref structure in the structure file. .
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
center: true
center_selection: System
fit: rot+trans
fit_selection: System
output_selection: System
pbc: mol
ur: compact
Docker config file
properties:
center: true
center_selection: System
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
fit: rot+trans
fit_selection: System
output_selection: System
pbc: mol
ur: compact
Singularity config file
properties:
center: true
center_selection: System
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
fit: rot+trans
fit_selection: System
output_selection: System
pbc: mol
ur: compact
Command line
gmx_image --config config_gmx_image.yml --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_image.xtc
JSON
Common config file
{
"properties": {
"fit_selection": "System",
"center_selection": "System",
"output_selection": "System",
"pbc": "mol",
"center": true,
"fit": "rot+trans",
"ur": "compact"
}
}
Docker config file
{
"properties": {
"fit_selection": "System",
"center_selection": "System",
"output_selection": "System",
"pbc": "mol",
"center": true,
"fit": "rot+trans",
"ur": "compact",
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"fit_selection": "System",
"center_selection": "System",
"output_selection": "System",
"pbc": "mol",
"center": true,
"fit": "rot+trans",
"ur": "compact",
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_image --config config_gmx_image.json --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_image.xtc
Cpptraj_image
Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file.
Get help
Command:
cpptraj_image -h
usage: cpptraj_image [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Corrects periodicity (image) from a given cpptraj trajectory file.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed trajectory.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing..
end (integer): (-1) Ending frame for slicing..
steps (integer): (1) Step for slicing..
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Command line
cpptraj_image --config config_cpptraj_image.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.image.netcdf
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf"
}
}
Docker config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_image --config config_cpptraj_image.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.image.netcdf
Gmx_rms
Wrapper of the GROMACS rms module for performing a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.
Get help
Command:
gmx_rms -h
usage: gmx_rms [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_xvg_path OUTPUT_XVG_PATH
Performs a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_index_path INPUT_INDEX_PATH
Path to the GROMACS index file. Accepted formats: ndx.
required arguments:
--input_structure_path INPUT_STRUCTURE_PATH
Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
--input_traj_path INPUT_TRAJ_PATH
Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
--output_xvg_path OUTPUT_XVG_PATH
Path to the XVG output file. Accepted formats: xvg.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_xvg_path (string): Path to the XVG output file. File type: output. Sample file. Accepted formats: XVG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
xvg (string): (none) XVG plot formatting. .
selection (string): (System) Group where the rms will be performed. If input_index_path provided, check the file for the accepted values. .
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
selection: System
Docker config file
properties:
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
selection: System
Singularity config file
properties:
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
selection: System
Command line
gmx_rms --config config_gmx_rms.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rms.xvg
JSON
Common config file
{
"properties": {
"selection": "System"
}
}
Docker config file
{
"properties": {
"selection": "System",
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"selection": "System",
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_rms --config config_gmx_rms.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rms.xvg
Gmx_cluster
Wrapper of the GROMACS cluster module for clustering structures from a given GROMACS compatible trajectory.
Get help
Command:
gmx_cluster -h
usage: gmx_cluster [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_pdb_path OUTPUT_PDB_PATH [--output_cluster_log_path OUTPUT_CLUSTER_LOG_PATH] [--output_rmsd_cluster_xpm_path OUTPUT_RMSD_CLUSTER_XPM_PATH] [--output_rmsd_dist_xvg_path OUTPUT_RMSD_DIST_XVG_PATH]
Creates cluster structures from a given GROMACS compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_index_path INPUT_INDEX_PATH
Path to the GROMACS index file. Accepted formats: ndx.
--output_cluster_log_path OUTPUT_CLUSTER_LOG_PATH
Path to the output log file. Accepted formats: log.
--output_rmsd_cluster_xpm_path OUTPUT_RMSD_CLUSTER_XPM_PATH
Path to the output xpm file. Accepted formats: xpm.
--output_rmsd_dist_xvg_path OUTPUT_RMSD_DIST_XVG_PATH
Path to the output xvg file. Accepted formats: xvg.
required arguments:
--input_structure_path INPUT_STRUCTURE_PATH
Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
--input_traj_path INPUT_TRAJ_PATH
Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
--output_pdb_path OUTPUT_PDB_PATH
Path to the output cluster file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_pdb_path (string): Path to the output cluster file. File type: output. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
output_cluster_log_path (string): Path to the output log file. File type: output. Sample file. Accepted formats: LOG
output_rmsd_cluster_xpm_path (string): Path to the output X PixMap compatible matrix file. File type: output. Sample file. Accepted formats: XPM
output_rmsd_dist_xvg_path (string): Path to xvgr/xmgr file. File type: output. Sample file. Accepted formats: XVG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
fit_selection (string): (System) Group where the fitting will be performed. If input_index_path provided, check the file for the accepted values. .
output_selection (string): (System) Group that is going to be written in the output trajectory. If input_index_path provided, check the file for the accepted values. .
dista (boolean): (False) Use RMSD of distances instead of RMS deviation..
nofit (boolean): (False) Do not use least squares fitting before RMSD calculation..
method (string): (linkage) Method for cluster determination. .
cutoff (number): (0.1) RMSD cut-off (nm) for two structures to be neighbor..
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
cutoff: 0.1
dista: false
fit_selection: System
method: linkage
output_selection: System
Docker config file
properties:
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
cutoff: 0.1
dista: false
fit_selection: System
method: linkage
output_selection: System
Singularity config file
properties:
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
cutoff: 0.1
dista: false
fit_selection: System
method: linkage
output_selection: System
Command line
gmx_cluster --config config_gmx_cluster.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb --output_cluster_log_path gmx_cluster_cluster.log --output_rmsd_cluster_xpm_path gmx_cluster_rmsd-clust.xpm --output_rmsd_dist_xvg_path gmx_cluster_rmsd-dist.xvg
JSON
Common config file
{
"properties": {
"fit_selection": "System",
"output_selection": "System",
"dista": false,
"method": "linkage",
"cutoff": 0.1
}
}
Docker config file
{
"properties": {
"fit_selection": "System",
"output_selection": "System",
"dista": false,
"method": "linkage",
"cutoff": 0.1,
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"fit_selection": "System",
"output_selection": "System",
"dista": false,
"method": "linkage",
"cutoff": 0.1,
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_cluster --config config_gmx_cluster.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb --output_cluster_log_path gmx_cluster_cluster.log --output_rmsd_cluster_xpm_path gmx_cluster_rmsd-clust.xpm --output_rmsd_dist_xvg_path gmx_cluster_rmsd-dist.xvg
Cpptraj_rgyr
Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_rgyr -h
usage: cpptraj_rgyr [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output analysis.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing..
end (integer): (-1) Ending frame for slicing..
steps (integer): (1) Step for slicing..
mask (string): (all-atoms) Mask definition. .
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:
end: -1
mask: c-alpha
start: 1
steps: 1
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: -1
mask: c-alpha
start: 1
steps: 1
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: -1
mask: c-alpha
start: 1
steps: 1
Command line
cpptraj_rgyr --config config_cpptraj_rgyr.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.rgyr.dat
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha"
}
}
Docker config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_rgyr --config config_cpptraj_rgyr.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.rgyr.dat
Cpptraj_strip
Wrapper of the Ambertools Cpptraj module for stripping a defined set of atoms (mask) from a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_strip -h
usage: cpptraj_strip [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Strips a defined set of atoms (mask) from a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed trajectory.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing..
end (integer): (-1) Ending frame for slicing..
steps (integer): (1) Step for slicing..
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: -1
format: netcdf
mask: c-alpha
start: 1
steps: 1
Command line
cpptraj_strip --config config_cpptraj_strip.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.strip.netcdf
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf"
}
}
Docker config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "netcdf",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_strip --config config_cpptraj_strip.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.strip.netcdf
Cpptraj_snapshot
Wrapper of the Ambertools Cpptraj module for extracting a particular snapshot from a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_snapshot -h
usage: cpptraj_snapshot [-h] --config CONFIG --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Extracts a particular snapshot from a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed structure.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed structure. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
snapshot (integer): (1) Frame to be captured for snapshot.
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
format: pdb
mask: c-alpha
snapshot: 12
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
format: pdb
mask: c-alpha
snapshot: 12
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
format: pdb
mask: c-alpha
snapshot: 12
Command line
cpptraj_snapshot --config config_cpptraj_snapshot.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.snapshot.pdb
JSON
Common config file
{
"properties": {
"snapshot": 12,
"mask": "c-alpha",
"format": "pdb"
}
}
Docker config file
{
"properties": {
"snapshot": 12,
"mask": "c-alpha",
"format": "pdb",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"snapshot": 12,
"mask": "c-alpha",
"format": "pdb",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_snapshot --config config_cpptraj_snapshot.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.snapshot.pdb
Gmx_energy
Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.
Get help
Command:
gmx_energy -h
usage: gmx_energy [-h] [--config CONFIG] --input_energy_path INPUT_ENERGY_PATH --output_xvg_path OUTPUT_XVG_PATH
Extracts energy components from a given GROMACS energy file.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_energy_path INPUT_ENERGY_PATH
Path to the input EDR file. Accepted formats: edr.
--output_xvg_path OUTPUT_XVG_PATH
Path to the XVG output file. Accepted formats: xvg.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_energy_path (string): Path to the input EDR file. File type: input. Sample file. Accepted formats: EDR
output_xvg_path (string): Path to the XVG output file. File type: output. Sample file. Accepted formats: XVG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
xvg (string): (none) XVG plot formatting. .
terms (array): ([Potential]) Energy terms. .
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
terms:
- Potential
- Pressure
Docker config file
properties:
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
terms:
- Potential
- Pressure
Singularity config file
properties:
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
terms:
- Potential
- Pressure
Command line
gmx_energy --config config_gmx_energy.yml --input_energy_path energy.edr --output_xvg_path ref_energy.xvg
JSON
Common config file
{
"properties": {
"terms": [
"Potential",
"Pressure"
]
}
}
Docker config file
{
"properties": {
"terms": [
"Potential",
"Pressure"
],
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"terms": [
"Potential",
"Pressure"
],
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_energy --config config_gmx_energy.json --input_energy_path energy.edr --output_xvg_path ref_energy.xvg
Gmx_trjconv_str_ens
Wrapper of the GROMACS trjconv module for extracting an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.
Get help
Command:
gmx_trjconv_str_ens -h
usage: gmx_trjconv_str_ens [-h] [--config CONFIG] --input_traj_path INPUT_TRAJ_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] --output_str_ens_path OUTPUT_STR_ENS_PATH
Extracts an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_index_path INPUT_INDEX_PATH
Path to the GROMACS index file. Accepted formats: ndx.
required arguments:
--input_traj_path INPUT_TRAJ_PATH
Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
--input_top_path INPUT_TOP_PATH
Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
--output_str_ens_path OUTPUT_STR_ENS_PATH
Path to the output file. Accepted formats: zip.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_str_ens_path (string): Path to the output file. File type: output. Sample file. Accepted formats: ZIP
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .
skip (integer): (1) Only write every nr-th frame..
start (integer): (0) Time of first frame to read from trajectory (default unit ps)..
end (integer): (0) Time of last frame to read from trajectory (default unit ps)..
dt (integer): (0) Only write frame when t MOD dt = first time (ps)..
output_name (string): (output) File name for ensemble of output files..
output_type (string): (pdb) File type for ensemble of output files. .
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
dt: 1
end: 10
output_name: output
output_type: pdb
selection: System
start: 0
Docker config file
properties:
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
dt: 1
end: 10
output_name: output
output_type: pdb
selection: System
start: 0
Singularity config file
properties:
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
dt: 1
end: 10
output_name: output
output_type: pdb
selection: System
start: 0
Command line
gmx_trjconv_str_ens --config config_gmx_trjconv_str_ens.yml --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_ens_path ref_trjconv.str.ens.zip
JSON
Common config file
{
"properties": {
"selection": "System",
"start": 0,
"end": 10,
"dt": 1,
"output_name": "output",
"output_type": "pdb"
}
}
Docker config file
{
"properties": {
"selection": "System",
"start": 0,
"end": 10,
"dt": 1,
"output_name": "output",
"output_type": "pdb",
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"selection": "System",
"start": 0,
"end": 10,
"dt": 1,
"output_name": "output",
"output_type": "pdb",
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_trjconv_str_ens --config config_gmx_trjconv_str_ens.json --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_ens_path ref_trjconv.str.ens.zip
Cpptraj_average
Wrapper of the Ambertools Cpptraj module for calculating a structure average of a given cpptraj compatible trajectory.
Get help
Command:
cpptraj_average -h
usage: cpptraj_average [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Calculates a structure average of a given cpptraj compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_top_path INPUT_TOP_PATH
Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
--input_traj_path INPUT_TRAJ_PATH
Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
--output_cpptraj_path OUTPUT_CPPTRAJ_PATH
Path to the output processed structure. Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP
input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB
output_cpptraj_path (string): Path to the output processed structure. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
start (integer): (1) Starting frame for slicing..
end (integer): (-1) Ending frame for slicing..
steps (integer): (1) Step for slicing..
mask (string): (all-atoms) Mask definition. .
format (string): (netcdf) Output trajectory format. .
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:
end: -1
format: pdb
mask: c-alpha
start: 1
steps: 1
Docker config file
properties:
container_image: afandiadib/ambertools:serial
container_path: docker
container_volume_path: /tmp
end: -1
format: pdb
mask: c-alpha
start: 1
steps: 1
Singularity config file
properties:
container_image: shub://bioexcel/ambertools_singularity
container_path: singularity
container_volume_path: /tmp
end: -1
format: pdb
mask: c-alpha
start: 1
steps: 1
Command line
cpptraj_average --config config_cpptraj_average.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.average.pdb
JSON
Common config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "pdb"
}
}
Docker config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "pdb",
"container_path": "docker",
"container_image": "afandiadib/ambertools:serial",
"container_volume_path": "/tmp"
}
}
Singularity config file
{
"properties": {
"start": 1,
"end": -1,
"steps": 1,
"mask": "c-alpha",
"format": "pdb",
"container_path": "singularity",
"container_image": "shub://bioexcel/ambertools_singularity",
"container_volume_path": "/tmp"
}
}
Command line
cpptraj_average --config config_cpptraj_average.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.average.pdb
Gmx_trjconv_str
Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.
Get help
Command:
gmx_trjconv_str -h
usage: gmx_trjconv_str [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] --output_str_path OUTPUT_STR_PATH
Converts between GROMACS compatible structure file formats and/or extracts a selection of atoms.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_index_path INPUT_INDEX_PATH
Path to the GROMACS index file. Accepted formats: ndx.
required arguments:
--input_structure_path INPUT_STRUCTURE_PATH
Path to the input structure file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
--input_top_path INPUT_TOP_PATH
Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
--output_str_path OUTPUT_STR_PATH
Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_str_path (string): Path to the output file. File type: output. Sample file. Accepted formats: PDB, XTC, TRR, CPT, GRO, G96, TNG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .
pbc (string): (mol) PBC treatment (see help text for full description) . .
center (boolean): (True) Center atoms in box..
ur (string): (compact) Unit-cell representation. .
fit (string): (none) Fit molecule to ref structure in the structure file. .
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
selection: System
Docker config file
properties:
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
selection: System
Singularity config file
properties:
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
selection: System
Command line
gmx_trjconv_str --config config_gmx_trjconv_str.yml --input_structure_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_path ref_trjconv.str.pdb
JSON
Common config file
{
"properties": {
"selection": "System"
}
}
Docker config file
{
"properties": {
"selection": "System",
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"selection": "System",
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_trjconv_str --config config_gmx_trjconv_str.json --input_structure_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_path ref_trjconv.str.pdb
Gmx_rgyr
Wrapper of the GROMACS gyrate module for computing the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.
Get help
Command:
gmx_rgyr -h
usage: gmx_rgyr [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_xvg_path OUTPUT_XVG_PATH
Computes the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_index_path INPUT_INDEX_PATH
Path to the GROMACS index file. Accepted formats: ndx.
required arguments:
--input_structure_path INPUT_STRUCTURE_PATH
Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
--input_traj_path INPUT_TRAJ_PATH
Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
--output_xvg_path OUTPUT_XVG_PATH
Path to the XVG output file. Accepted formats: xvg.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT
input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG
input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX
output_xvg_path (string): Path to the XVG output file. File type: output. Sample file. Accepted formats: XVG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
xvg (string): (none) XVG plot formatting. .
selection (string): (System) Group where the rgyr will be performed. If input_index_path provided, check the file for the accepted values. .
binary_path (string): (gmx) Path to the GROMACS 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): (gromacs/gromacs:2022.2) 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:
selection: System
Docker config file
properties:
container_image: gromacs/gromacs:2022.2
container_path: docker
container_user_id: '1001'
container_volume_path: /tmp
selection: System
Singularity config file
properties:
container_image: shub://michael-tn/gromacs
container_path: singularity
container_volume_path: /tmp
selection: System
Command line
gmx_rgyr --config config_gmx_rgyr.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rgyr.xvg
JSON
Common config file
{
"properties": {
"selection": "System"
}
}
Docker config file
{
"properties": {
"selection": "System",
"container_path": "docker",
"container_image": "gromacs/gromacs:2022.2",
"container_volume_path": "/tmp",
"container_user_id": "1001"
}
}
Singularity config file
{
"properties": {
"selection": "System",
"container_path": "singularity",
"container_image": "shub://michael-tn/gromacs",
"container_volume_path": "/tmp"
}
}
Command line
gmx_rgyr --config config_gmx_rgyr.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rgyr.xvg