aiida-amber

AiiDA plugin that wraps amber molecular dynamics executables

status stable

AiiDA >=2.6.1,<=2.6.3

General information

Install pip install aiida-amber

Source code https://github.com/CCPBioSim/aiida-amber

Documentation https://aiida-amber.readthedocs.io/

Contact Jas Kalayan <jas.kalayan@stfc.ac.uk>

Python import import aiida_amber

Latest version 2.2.0

Released 2026-03-02

Registry checks

W008: Unable to reach documentation URL: https://aiida-amber.readthedocs.io/

Click any code (W001, E001…) to jump to troubleshooting instructions .

Plugins provided

Calculations 5 Parsers 5 Data 7 Console scripts 5

Entry points

CalcJobs and calculation functions aiida.calculations

amber.antechamber

AiiDA calculation plugin wrapping the antechamber executable. AiiDA plugin wrapper for the amber 'antechamber' command.

Input	Required	Valid types	Description
`input_file`	true	`SinglefileData`	input structure file for antechamber
`parameters`	true	`AntechamberParameters`	Command line parameters for antechamber
`additional_file`	false	`SinglefileData, NoneType`	additional file
`antechamber_outfiles`	false	`List, NoneType`	List of antechamber output file names.
`charge_file`	false	`SinglefileData, NoneType`	charge file
`check_file`	false	`SinglefileData, NoneType`	check file for gaussian
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`esp_file`	false	`SinglefileData, NoneType`	gaussian esp file
`metadata`	false
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`remote_folder`	false	`RemoteData, NoneType`	Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.
`res_top_file`	false	`SinglefileData, NoneType`	residue toplogy file

Output	Required	Valid types	Description
`output_file`	true	`SinglefileData`	output file
`remote_folder`	true	`RemoteData`	Input files necessary to run the process will be stored in this folder node.
`retrieved`	true	`FolderData`	Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
`stdout`	true	`SinglefileData`	stdout
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.
100	The process did not have the required `retrieved` output.
110	The job ran out of memory.
120	The job ran out of walltime.
131	The specified account is invalid.
140	The node running the job failed.
150	{message}
300	Calculation did not produce all expected output files.

amber.parmed

AiiDA calculation plugin wrapping the parmed executable. AiiDA plugin wrapper for the amber 'parmed' command.

Input	Required	Valid types	Description
`parameters`	true	`ParmedParameters`	Command line parameters for parmed
`parmed_script`	true	`SinglefileData`	input file for parmed commands
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`inpcrd_files`	false	`SinglefileData`	List of inpcrd files to load into ParmEd
`metadata`	false
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`parmed_dirs`	false	`FolderData`	path to directory where inputs referenced in parmed input file are
`parmed_inpfiles`	false	`SinglefileData`	inputs referenced in parmed input script
`parmed_outfiles`	false	`List, NoneType`	List of parmed output file names.
`prmtop_files`	false	`SinglefileData`	List of topology files to load into ParmEd
`remote_folder`	false	`RemoteData, NoneType`	Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.

Output	Required	Valid types	Description
`remote_folder`	true	`RemoteData`	Input files necessary to run the process will be stored in this folder node.
`retrieved`	true	`FolderData`	Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
`stdout`	true	`SinglefileData`	stdout
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.
100	The process did not have the required `retrieved` output.
110	The job ran out of memory.
120	The job ran out of walltime.
131	The specified account is invalid.
140	The node running the job failed.
150	{message}
300	Calculation did not produce all expected output files.

amber.pdb4amber

AiiDA calculation plugin wrapping the pdb4amber executable. AiiDA plugin wrapper for the amber 'pdb4amber' command.

Input	Required	Valid types	Description
`input_file`	true	`SinglefileData`	input pdb file for pdb4amber
`parameters`	true	`Pdb4amberParameters`	Command line parameters for pdb4amber
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`metadata`	false
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`pdb4amber_outfiles`	false	`List, NoneType`	List of pdb4amber output file names.
`remote_folder`	false	`RemoteData, NoneType`	Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.

Output	Required	Valid types	Description
`output_file`	true	`SinglefileData`	outputted pdb file
`remote_folder`	true	`RemoteData`	Input files necessary to run the process will be stored in this folder node.
`retrieved`	true	`FolderData`	Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
`stdout`	true	`SinglefileData`	stdout
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.
100	The process did not have the required `retrieved` output.
110	The job ran out of memory.
120	The job ran out of walltime.
131	The specified account is invalid.
140	The node running the job failed.
150	{message}
300	Calculation did not produce all expected output files.

amber.sander

AiiDA calculation plugin wrapping the sander executable. AiiDA plugin wrapper for the amber 'sander' command.

Input	Required	Valid types	Description
`inpcrd`	true	`SinglefileData`	input initial coordinates and (optionally) velocities and periodic box size.
`mdin`	true	`SinglefileData`	input control data for the min/md run.
`parameters`	true	`SanderParameters`	Command line parameters for sander
`prmtop`	true	`SinglefileData`	input molecular topology, force field, periodic box type, atom and residue names.
`cein`	false	`SinglefileData, NoneType`	input redox state definitions.
`cerestrt`	false	`SinglefileData, NoneType`	redox state definitions, final redox states for restart (same format as cein).
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`cpin`	false	`SinglefileData, NoneType`	input protonation state definitions.
`cprestrt`	false	`SinglefileData, NoneType`	protonation state definitions, final protonation states for restart (same format as cpin).
`evbin`	false	`SinglefileData, NoneType`	input input for EVB potentials.
`inpdip`	false	`SinglefileData, NoneType`	input polarizable dipole file, when indmeth=3.
`inptraj`	false	`SinglefileData, NoneType`	input coordinate sets in trajectory format, when imin=5 or 6.
`metadata`	false
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`mtmd`	false	`SinglefileData, NoneType`	input (optional) containing list of files and parameters for targeted MD to multiple targets.
`refc`	false	`SinglefileData, NoneType`	input (optional) reference coords for position restraints; also used for targeted MD.
`remote_folder`	false	`RemoteData, NoneType`	Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.

Output	Required	Valid types	Description
`mdinfo`	true	`SinglefileData`	output latest mdout-format energy info.
`mdout`	true	`SinglefileData`	output user readable state info and diagnostics -o stdout will send output to stdout (to the terminal) instead of to a file.
`remote_folder`	true	`RemoteData`	Input files necessary to run the process will be stored in this folder node.
`retrieved`	true	`FolderData`	Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
`stdout`	true	`SinglefileData`	stdout
`ceout`	false	`SinglefileData`	output redox state data saved over trajectory.
`cpout`	false	`SinglefileData`	output protonation state data saved over trajectory.
`mdcrd`	false	`SinglefileData`	output coordinate sets saved over trajectory.
`mden`	false	`SinglefileData`	output extensive energy data over trajectory (not synchronized with mdcrd or mdvel).
`mdfrc`	false	`SinglefileData`	output force sets saved over trajectory.
`mdvel`	false	`SinglefileData`	output velocity sets saved over trajectory.
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.
`restrt`	false	`SinglefileData`	output final coordinates, velocity, and box dimensions if any - for restarting run.
`rstdip`	false	`SinglefileData`	output polarizable dipole file, when indmeth=3.
`suffix`	false	`str`	output this string will be added to all unspecified output files that are printed (for multisander runs, it will append this suffix to all output files).

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.
100	The process did not have the required `retrieved` output.
110	The job ran out of memory.
120	The job ran out of walltime.
131	The specified account is invalid.
140	The node running the job failed.
150	{message}
300	Calculation did not produce all expected output files.

amber.tleap

AiiDA calculation plugin wrapping the tleap executable. AiiDA plugin wrapper for the amber 'tleap' command.

Input	Required	Valid types	Description
`parameters`	true	`TleapParameters`	Command line parameters for tleap
`tleapscript`	true	`SinglefileData`	input file for tleap commands
`code`	false	`AbstractCode, NoneType`	The `Code` to use for this job. This input is required, unless the `remote_folder` input is specified, which means an existing job is being imported and no code will actually be run.
`dirs`	false	`FolderData`	path to directory where custom leaprc are
`metadata`	false
`monitors`	false	`Dict`	Add monitoring functions that can inspect output files while the job is running and decide to prematurely terminate the job.
`remote_folder`	false	`RemoteData, NoneType`	Remote directory containing the results of an already completed calculation job without AiiDA. The inputs should be passed to the `CalcJob` as normal but instead of launching the actual job, the engine will recreate the input files and then proceed straight to the retrieve step where the files of this `RemoteData` will be retrieved as if it had been actually launched through AiiDA. If a parser is defined in the inputs, the results are parsed and attached as output nodes as usual.
`tleap_dirs`	false	`FolderData`	path to directory where inputs referenced in tleap input file are
`tleap_inpfiles`	false	`SinglefileData`	inputs referenced in tleap input file
`tleap_outfiles`	false	`List, NoneType`	List of tleap output file names.

Output	Required	Valid types	Description
`remote_folder`	true	`RemoteData`	Input files necessary to run the process will be stored in this folder node.
`retrieved`	true	`FolderData`	Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
`stdout`	true	`SinglefileData`	stdout
`remote_stash`	false	`RemoteStashData`	Contents of the `stash.source_list` option are stored in this remote folder after job completion.

Exit status	Message
1	The process has failed with an unspecified error.
2	The process failed with legacy failure mode.
10	The process returned an invalid output.
11	The process did not register a required output.
100	The process did not have the required `retrieved` output.
110	The job ran out of memory.
120	The job ran out of walltime.
131	The specified account is invalid.
140	The node running the job failed.
150	{message}
300	Calculation did not produce all expected output files.

Data node types aiida.data

amber.antechamber
aiida_amber.data.antechamber:AntechamberParameters
amber.parmed
aiida_amber.data.parmed:ParmedParameters
amber.parmed_input
aiida_amber.data.parmed_input:ParmedInputData
amber.pdb4amber
aiida_amber.data.pdb4amber:Pdb4amberParameters
amber.sander
aiida_amber.data.sander:SanderParameters
amber.tleap
aiida_amber.data.tleap:TleapParameters
amber.tleap_input
aiida_amber.data.tleap_input:TleapInputData

CalcJob parsers aiida.parsers

amber.antechamber
aiida_amber.parsers.antechamber:AntechamberParser
amber.parmed
aiida_amber.parsers.parmed:ParmedParser
amber.pdb4amber
aiida_amber.parsers.pdb4amber:Pdb4amberParser
amber.sander
aiida_amber.parsers.sander:SanderParser
amber.tleap
aiida_amber.parsers.tleap:TleapParser

Console scripts console_scripts

aiida_antechamber
aiida_amber.cli.antechamber:cli
aiida_parmed
aiida_amber.cli.parmed:cli
aiida_pdb4amber
aiida_amber.cli.pdb4amber:cli
aiida_sander
aiida_amber.cli.sander:cli
aiida_tleap
aiida_amber.cli.tleap:cli