MDKit is a python package that allows to easily perform MD simulations with Amber. MDKit is especially helpful thanks to its prepare_md.py routine which can set up all the steps required for MD: system preparation with or without ligands, 2 steps of minimization, equilibration in NVT ensemble, equilibration in NPT ensemble. prepare_md.py can be used to run MD on globular proteins or embedded membrane proteins (prepared with NAMD GUI) and to run standard or accelerated MD.
Versions of Amber supported by MDKit
Currently, only Amber14 and Amber16 are supported. Notably, AmberTools should also be installed (versions 14-17).
The easiest way to install MDKit is to create a virtual environment. In this way, MDKit and its dependencies can easily be installed in user-space without clashing with potentially incompatible system-wise packages.
Once virtualenv has been properly installed, simply type (and press the return key)
virtualenv envon the command line followed by
source env/bin/activateto activate the virtual environment (do not forget to activate your environment every time you log into a new shell environment).
Finally, the MDKit package can be set up by going in MDKit installation directory and typing:
python setup.py installInstallation is complete!