Install EnzyHTP 

This guide leads you through steps of installing EnzyHTP

I. Make a new environment 

We recommand using conda to manage the enviroment of EnzyHTP.
Make sure you installed and activate conda before running the following command.
You can find many good tutorial of conda installation elsewhere.

conda create --name enzy_htp python=3.9
conda activate enzy_htp

This creates a conda environment called enzy_htp and we will install python package EnzyHTP needs in it.

You can activate this enviroment anytime when you need to use EnzyHTP by conda activate enzy_htp

II. Install EnzyHTP 

There are 2 ways of installing EnzyHTP: 1) from conda 2) from source

Note

Make sure you are under the correct environment when doing this step

a. Install from conda 

Currently we recommend installing from conda.
conda install enzy_htp -c yang_lab -c conda-forge

b. Install from source 

Obtain the source code

EnzyHTP is shared-source on GitHub.
git clone https://github.com/ChemBioHTP/EnzyHTP.git
This will generate a folder name “EnzyHTP” containing the source code under where you run this command.

Note

Note that the source code version when writing this tutorial is stored as a release too. (try this version if this tutorial fails with the most current version)

Install Python packages
cd EnzyHTP # this is what you created via clone in the previous step
source dev-tools/conda-install

III. Install External Dependencies 

EnzyHTP use Amber as one of the MD engine (currently the only one). You need to install Amber if you want to enable MD/mutation functions in EnzyHTP. AmberTools is free (CPU only) and Amber is charged (GPU support). Most universities have Amber purchased and installed in their local clusters. Contact your local cluster if you don’t know how to load/setup the installed Amber.

As an example, here is the command for loading Amber in our local cluster ACCRE.

source /home/shaoq1/bin/amber_env/amber-accre.sh

2. Install Gaussian16 (optional)

EnzyHTP use Gaussian16 as one of the QM engine (currently the only one). You need to install Gaussian16 if you want to enable QM-based functions in EnzyHTP. Gaussian16 is charged. Most universities have Gaussian16 purchased and installed in their local clusters. Contact your local cluster if you don’t know how to load/setup the installed Gaussian16.

As an example, here is the command for loading Gaussian16 in our local cluster ACCRE.

module load Gaussian/16.B.01

3. Install Multiwfn (optional)

EnzyHTP use Multiwfn as one of the wavefunction analysis engine.
You need to install Multiwfn if you want to enable wavefunction analysis functions in EnzyHTP.
Multiwfn is free and very easy to install.

Download and follow section 2.1.2 of their manual to install

Multiwfn Download page: http://sobereva.com/multiwfn/

Note

Some HPC may not have the most up-to-date library for running Multiwfn For example, on our local cluster ACCRE, these module needs to be load for Multiwfn to run on a computing node.

module load GCC/6.4.0-2.28  OpenMPI/2.1.1

4. Install Rosetta (optional)

EnzyHTP use Rosetta as one of the post-analysis & docking engine.
You need to install Rosetta if you want to enable docking & analysis (e.g.: thermostability assessment) functions in EnzyHTP.
Rosetta is free and easy to install.

Follow this page for the install:

https://new.rosettacommons.org/demos/latest/tutorials/install_build/install_build

Author: QZ Shao <shaoqz@icloud.com>