phd3

Protein Hybrid Discrete Dynamics/DFT. Quantum Mechanical/Discrete Molecular Dynamics engine to provide rapid sampling of metalloenzymes.

System Requirements

• TURBOMOLE Version 6.6
• piDMD
• Openbabel Version 2.4.0
• Chimera Version 1.6.0 or greater (1.15.0 or greater recommended)
• Python Version 3.6 or greater (3.8 or greater recommended)

Python Package Dependencies

When phd3 is installed via pip, the following packages will also be installed if not already present on your system.

• jinja2
• sklearn
• propka
• numpy Version 1.20.0 or greater
• hdbscan
• scipy Version 1.1.0

Installation

First, clone this repository

git clone https://github.com/alexandrova-lab-ucla/phd3

Then, edit the phd_config.json file so that all of the paths in the PATHS section point to the correct directory. That is

• TURBODIR points to the TURBOMOLE directory that contains basen, bin, TURBOTEST, Config_turbo_env, etc.
• DMD_DIR points to the directory that holds the DMD binaries complex.linux, comples_m2p.linux, pdmd.linux, and repdmd.linux.
• parameters points to the directory that holds the DMD parameters file allatom.par, DMD_NA_allatom.par, etc.
• chimera points to the directory that holds the chimera executable. Note, this is not the path TO the chimera executable, but to the directory that contains the executable.

If you are using phd3 on a cluster with queuing, you can modify the QUEUING section as well. Next we make a directory in ~/.config and moves some files there as

mkdir ${HOME}/.config/phd3
mv phd_config.json logger_config.json phd3/templates/submit.j2 ${HOME}/.config/phd3

In order to prevent Turbomole from failing, you may need to add the following to your .bashrc. This tells the CPU to use a math library that TURBOMOLE depends on. If this is not used, TURBOMOLE will segfault, even in define.

module load mkl
export MKL_DEBUG_CPU_TYPE=5

Finally, we use pip3 to install

pip3 install ./

If you are having issues with 'sudo', add the --user option. Further, if you are developing, include the -e option as

pip3 install --user -e ./

Make sure that ~/.local/bin is in your PATH as this is where the executibles are installed with pip3.

Usage

The following scripts are available after installation

• setupphd.py
• runphd.py
• submitphd.py
• submitdmd.py
• setupturbomole.py
• runturbomole.py
• submitturbomole.py
• tfe.py
• relabelpdb.py
• setupdmd.py
• rundmd.py
• m2p.py
• cutqm.py

See the wiki for a detailed user guide on how to run various calculations.

Citation

Please cite the following papers if you use QM/DMD in your research on top of the TURBOMOLE and piDMD citations.

M. Sparta, D. Shirvanyants, F. Ding, N. V. Dokholyan, A. N. Alexandrova. "Hybrid Dynamics Simulation Engine for Metalloproteins" Biophys J 103: 4 (2012).

N. M. Gallup, A. N. Alexandrova. "Use of QM/DMD as a Multiscale Approach to Modeling Metalloenzymes" Methods Enzymol 577 (2016).

If you use the titratable DMD in your work, please cite the following in your research as well as propka

D. R. Reilley, J. Wang, N. Dokholyan, A. N. Alexandrova. "Titr-DMD - A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework" (Submitted 2021).