Command-line
xBFreE command-line¶
xBFreE uses subcommands to execute different BFE methods for different MD programs:
fast →💬 All flags available in **xBFreE** are shown below:
xbfree -h
usage: xbfree [-h] [-v] {gmx_MMPBSA,amber_MMPBSA,namd_MMPBSA,charmm_MMPBSA} ...
xBFreEnergy is a tool to compute Binding Free Energy with different methods
positional arguments:
{gmx_MMPBSA,amber_MMPBSA,namd_MMPBSA,charmm_MMPBSA}
Methods to compute Binding Free Energy
gmx_MMPBSA PB and other implicit solvent-based calculations for GROMACS
amber_MMPBSA PB and other implicit solvent-based calculations for AMBER
namd_MMPBSA PB and other implicit solvent-based calculations for NAMD
charmm_MMPBSA PB and other implicit solvent-based calculations for CHARMM
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
xBFreEnergy is a tool to compute Binding Free Energy with different methods
restart ↻
xbfree -h
usage: xbfree [-h] [-v] {gmx_MMPBSA,amber_MMPBSA,namd_MMPBSA,charmm_MMPBSA} ...
xBFreEnergy is a tool to compute Binding Free Energy with different methods
positional arguments:
{gmx_MMPBSA,amber_MMPBSA,namd_MMPBSA,charmm_MMPBSA}
Methods to compute Binding Free Energy
gmx_MMPBSA PB and other implicit solvent-based calculations for GROMACS
amber_MMPBSA PB and other implicit solvent-based calculations for AMBER
namd_MMPBSA PB and other implicit solvent-based calculations for NAMD
charmm_MMPBSA PB and other implicit solvent-based calculations for CHARMM
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
xBFreEnergy is a tool to compute Binding Free Energy with different methods
restart ↻
Sub-commands structure¶
Each subcommand contains its own arguments according to the MD program and method selected. However, we decide to make some arguments redundant to simplify the command-line instructions and keep it similar to gmx_MMPBSA:
fast →💬 All flags available in **xBFreE** are shown below:
xbfree gmx_MMPBSA -h
usage: ...
This is the core of gmx_MMPBSA and it will perfrom all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< Gromacs specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
xbfree gmx_MMPBSA -h
usage: ...
This is the core of gmx_MMPBSA and it will perfrom all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< Gromacs specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
fast →💬 All flags available in **xBFreE** are shown below:
xbfree amber_MMPBSA -h
usage: ...
This is the core of amber_MMPBSA and it will perform all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< Amber specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
xbfree amber_MMPBSA -h
usage: ...
This is the core of amber_MMPBSA and it will perform all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< Amber specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
fast →💬 All flags available in **xBFreE** are shown below:
xbfree namd_MMPBSA -h
usage: ...
This is the core of namd_MMPBSA and it will perform all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< NAMD specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
xbfree namd_MMPBSA -h
usage: ...
This is the core of namd_MMPBSA and it will perform all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< NAMD specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
fast →💬 All flags available in **xBFreE** are shown below:
xbfree charmm_MMPBSA -h
usage: ...
This is the core of charmm_MMPBSA and it will perform all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< CHARMM specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
xbfree charmm_MMPBSA -h
usage: ...
This is the core of charmm_MMPBSA and it will perform all the calculations
optional arguments:
-h, --help show this help message and exit
-O, --overwrite Allow output files to be overwritten
--create_input [{gb,pb,rism,ala,decomp,nmode,gbnsr6,all} ...]
Create an new input file with selected calculation type.
--rewrite-output Do not re-run any calculations, just parse the output files from the previous calculation and rewrite the output files.
-s, --stability Perform stability calculation. Only the complex parameters are required. In any other case receptor and ligand parameters will be ignored
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-v, --version show program's version number and exit
Input and Output Files:
These options specify the input files and optional output files.
-i FILE MM/PBSA input file.
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE Output file with statistics for the selected method.
-do FILE Output file for decomposition statistics summary.
-eo FILE CSV-format output of all energy terms for every frame in every calculation. File name forced to end in [.csv]. This file is only written when specified on the command-line.
-deo FILE CSV-format output of all energy terms for each printed residue in decomposition calculations. File name forced to end in [.csv]. This file is only written when specified on the command-line.
< CHARMM specific arguments >
Miscellaneous Options:
-prefix
Prefix for intermediate files.
--input-file-help Print all available options in the input file.
--clean Clean temporary files and quit.
xBFreEnergy is a tool to compute Binding Free Enrgy with different methods
1 year ago2023-07-12 2 years ago2023-05-27