sander package
Submodules
sander.sander_mdrun module
Module containing the SanderMDRun class and the command line interface.
- class sander.sander_mdrun.SanderMDRun(input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str, input_ref_path: str | None = None, input_mdin_path: str | None = None, input_cpin_path: str | None = None, output_cpout_path: str | None = None, output_cprst_path: str | None = None, output_mdinfo_path: str | None = None, properties: dict | None = None, **kwargs)[source]
Bases:
BiobbObject
biobb_amber SanderMDRunWrapper of the AmberTools (AMBER MD Package) sander tool module.Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package.- Parameters:
input_top_path (str) – Input topology file (AMBER ParmTop). File type: input. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).
input_crd_path (str) –
Input coordinates file (AMBER crd). File type: input. Sample file. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).
input_mdin_path (str) (Optional) –
Input configuration file (MD run options) (AMBER mdin). File type: input. Sample file. Accepted formats: mdin (edam:format_2330), in (edam:format_2330), txt (edam:format_2330).
input_cpin_path (str) (Optional) –
Input constant pH file (AMBER cpin). File type: input. Sample file. Accepted formats: cpin (edam:format_2330).
input_ref_path (str) (Optional) –
Input reference coordinates for position restraints. File type: input. Sample file. Accepted formats: rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886), crd (edam:format_3878).
output_log_path (str) –
Output log file. File type: output. Sample file. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).
output_traj_path (str) –
Output trajectory file. File type: output. Sample file. Accepted formats: trj (edam:format_3878), crd (edam:format_3878), mdcrd (edam:format_3878), x (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650).
output_rst_path (str) –
Output restart file. File type: output. Sample file. Accepted formats: rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).
output_cpout_path (str) (Optional) –
Output constant pH file (AMBER cpout). File type: output. Sample file. Accepted formats: cpout (edam:format_2330).
output_cprst_path (str) (Optional) –
Output constant pH restart file (AMBER rstout). File type: output. Sample file. Accepted formats: cprst (edam:format_3886), rst (edam:format_3886), rst7 (edam:format_3886).
output_mdinfo_path (str) (Optional) –
Output MD info. File type: output. Sample file. Accepted formats: mdinfo (edam:format_2330).
properties (dict - Python dictionary object containing the tool parameters, not input/output files) –
mdin (dict) - ({}) Sander MD run options specification. (Used if input_mdin_path is None)
simulation_type (str) - (“minimization”) Default options for the mdin file. Each creates a different mdin file. Values: minimization (Runs an energy minimization), min_vacuo (Runs an energy minimization in vacuo), NVT (Runs an NVT equilibration), npt (Runs an NPT equilibration), free (Runs a MD simulation), heat (Heats the MD system).
binary_path (str) - (“sander”) sander binary path to be used.
direct_mdin (bool) - (False) Use input_mdin_path as it is, skip file parsing.
mpi_bin (str) - (None) Path to the MPI runner. Usually “mpirun” or “srun”.
mpi_np (int) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1.
mpi_flags (str) - (None) Path to the MPI hostlist file.
remove_tmp (bool) - (True) [WF property] Remove temporal files.
restart (bool) - (False) [WF property] Do not execute if output files exist.
sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.
container_path (str) - (None) Container path definition.
container_image (str) - (‘afandiadib/ambertools:serial’) Container image definition.
container_volume_path (str) - (‘/tmp’) Container volume path definition.
container_working_dir (str) - (None) Container working directory definition.
container_user_id (str) - (None) Container user_id definition.
container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.
Examples
This is a use example of how to use the building block from Python:
from biobb_amber.sander.sander_mdrun import sander_mdrun prop = { 'simulation_type' : 'minimization', 'mdin' : { 'dt' : 0.002 } } sander_mdrun(input_top_path='/path/to/topology.top', input_crd_path='/path/to/coordinates.crd', output_traj_path='/path/to/newTrajectory.crd', output_rst_path='/path/to/newRestart.rst', output_log_path='/path/to/newAmberlog.log', properties=prop)
- Info:
- wrapped_software:
name: AmberTools Sander
version: >20.9
license: LGPL 2.1
multinode: mpi
- ontology:
name: EDAM
schema: http://edamontology.org/EDAM.owl
- sander.sander_mdrun.sander_mdrun(input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str, input_mdin_path: str | None = None, input_cpin_path: str | None = None, output_cpout_path: str | None = None, output_cprst_path: str | None = None, output_mdinfo_path: str | None = None, input_ref_path: str | None = None, properties: dict | None = None, **kwargs) int [source]
Create
SanderMDRun
method