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
/bin/sh: cpptraj_slice: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: cpptraj_convert: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: cpptraj_dry: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: cpptraj_rmsf: command not found

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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: gmx_trjconv_trj: command not found

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_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)..
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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_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:latest",
    "container_volume_path": "/tmp"
  }
}

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_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
/bin/sh: cpptraj_mask: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: cpptraj_rms: command not found

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, 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. .
  • cpptraj_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..
  • 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

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

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
/bin/sh: cpptraj_bfactor: command not found

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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: gmx_image: command not found

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. .
  • 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. .
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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:latest",
    "container_volume_path": "/tmp"
  }
}

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
/bin/sh: cpptraj_image: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: gmx_rms: command not found

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. .
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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:latest",
    "container_volume_path": "/tmp"
  }
}

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
/bin/sh: gmx_cluster: command not found

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

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..
  • method (string): (linkage) Method for cluster determination. .
  • cutoff (number): (0.1) RMSD cut-off (nm) for two structures to be neighbor..
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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

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:latest",
    "container_volume_path": "/tmp"
  }
}

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

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
/bin/sh: cpptraj_rgyr: command not found

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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: cpptraj_strip: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: cpptraj_snapshot: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: gmx_energy: command not found

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. .
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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:latest",
    "container_volume_path": "/tmp"
  }
}

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
/bin/sh: gmx_trjconv_str_ens: command not found

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. .
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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:latest",
    "container_volume_path": "/tmp"
  }
}

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
/bin/sh: cpptraj_average: command not found

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, 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, 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. .
  • cpptraj_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..
  • 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
/bin/sh: gmx_trjconv_str: command not found

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: 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. .
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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:latest",
    "container_volume_path": "/tmp"
  }
}

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
/bin/sh: gmx_rgyr: command not found

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. .
  • gmx_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..
  • container_path (string): (None) Container path definition..
  • container_image (string): (gromacs/gromacs:latest) 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:latest
  container_path: docker
  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:latest",
    "container_volume_path": "/tmp"
  }
}

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