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The AMBRose python module was developed by Maria Szegedy (Khare Lab), Kristin Blacklock (Khare Lab), and Hai Nguyen (Case Lab) at Rutgers University.

Last updated August 28, 2019.

For questions please contact:

Why AMBRose?

Have you ever wanted Rosetta to seamlessly make an MD simulation of your structure and use frames from it in your protocol? Or just wished you could automate the creation of MD input files? If so, AMBRose is the PyRosetta companion module for you. With AMBRose, obtaining MD data can be as easy as setting up a mover! Download AMBRose today and see what MD can do for your project. (No actual movers were harmed in the making of this software.)

Description

This module provides several functions for intercompatibility between AMBER and Rosetta, with major functions being:

  • The conversion of a pose to starting coordinates for sander/PMEMD
  • The dumping of LEaP-safe PDB files from poses
  • The minimization and simulation of poses in sander/PMEMD without having to explicitly work with AMBER constructs
  • The conversion of trajectories to series of poses

For the full API, see the docstrings of AMBRose's modules and objects. These will be turned into readthedocs.io documentation eventually.

System Requirements

Make sure your environment variable $AMBERHOME is set to the directory where AMBER lives. (This is the directory where bin/pmemd.CUDA lives, where amber.sh lives, et cetera.)

For legacy only:

The limitations of AMBRose

AMBRose can work with (i.e. convert from one medium to another) any of three things:

  • Canonical proteins
  • Canonical RNAs
  • Canonical DNAs

Anything beyond this (ligands, noncanonical residues, most post-translational modifications) will almost certainly fail to be converted.

AMBRose's movers currently only run minimizations and simulations on the GPU, with pmemd.cuda. This is not a huge problem, because GPU computation is the state of the art for AMBER, and all the AMBER devs are currently focused on it. However, if for whatever reason you need CPU computation instead, they can be set to do that, but they will only be able to run on one core in most cases. This issue is not likely to be solved.

How to install AMBRose

Automatically

Currently, you can install AMBRose with anything capable of handling a setup.py script, such as pip. If you are taking this route, you must first clone RosettaCommons/tools, and then navigate to the directory tools/AmbRose. Here, run

$ pip install --user .

which will copy the folder ambrose to the correct place in your PYTHONPATH.

Manually

If you know where in your PYTHONPATH you want to keep AMBRose, you can copy the directory tools/AmbRose/ambrose directly to wherever you need it to be. Just make sure it's somewhere in one of the folders in your PYTHONPATH.

How to use AMBRose

First, import PyRosetta and AMBRose:

>>> import pyrosetta as pr; pr.init()
>>> import ambrose

Exploring the AMBRose API

AMBRose's API is currently best explored through its docstrings. These are accessible through the help() function:

>>> help(ambrose)

If you want to read the docstrings in a specific submodule or pertaining to a specific object, that can be help()ed too:

>>> help(ambrose.pose_selectors)
>>> help(ambrose.AMBERSimulateMover)

Turning poses into input files

AMBRose can turn a pose into input files for sander/PMEMD. To do this, use the function pose_to_amber_params:

>>> pose = pr.pose_from_file('my-protein.pdb')
>>> ambrose.pose_to_amber_params(pose,
...                              crd_path='my-protein.rst7',
...                              top_path='my-protein.parm7')

This will create the files my-protein.rst7 and my-protein.parm7, which can be used as starting coordinates for sander/PMEMD. Additional arguments may be given to control the solvation of the pose; see the output of the command help(ambrose.pose_to_amber_params).

Turning trajectories into poses

AMBRose can read a trajectory and output the frames as poses. To do this, you must first import the AmberTools module pytraj, and read in your trajectory as a Trajectory object. Then, you can use AMBRose's TrajToPoses object to turn it into a sequence of poses:

>>> import pytraj as pt
>>> traj = pt.iterload('my-protein.rst7', 'my-protein.parm7')
>>> poses = ambrose.TrajToPoses(traj)

TrajToPoses objects can be indexed and sliced like any sequence. Their elements are poses corresponding to each successive frame of the trajectory that they were made from. For example, to get a pose corresponding to the last frame of a trajectory, you can run the previous code, and then:

>>> pose = poses[-1]

Simulating a pose without touching AMBER

AMBRose's "movers" (which aren't real movers, but are built to function like them) are intended to abstract away the entire process of converting to AMBER, simulating a pose, converting the frames back, and selecting a frame. AMBERSimulateMover does exactly this. When its apply() is called on a pose, it creates and runs a simulation with the parameters you have specified, and replaces the pose with the last frame of the simulation's trajectory. Here is an example where we simulate a pose for 10 ps at 303 K (but starting from 273 K), with an explicit solvent, and replace it with the last frame of the simulation:

>>> pose = pr.pose_from_file('my-protein.pdb')
>>> mover = ambrose.AMBERSimulateMover()
>>> mover.duration = 10.     # 10 picoseconds
>>> mover.temperature = 303. # 303 kelvin
>>> mover.starting_temperature = 273.
>>> mover.solvent = ambrose.Solvents.SPCE_WATER
>>> mover.working_dir = 'my-simulation-dir'
>>> mover.prefix = 'my-simulation'
>>> mover.apply(pose) # overwrites pose and creates many files in my-simulation-dir

You can change which pose is selected by overwriting the mover's pose_selector. See the submodule ambrose.pose_selectors for what pose selector functions should look like.