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Malgorzata Biczysko edited this page Oct 28, 2023 · 9 revisions

Installation

Phenix

Please first install PHENIX, see https://www.phenix-online.org/

Once you have PHENIX installed, go to the directory where you installed PHENIX.

 source phenix_env.sh
 phenix.python modules/cctbx_project/libtbx/auto_build/bootstrap.py --builder=qrefine

Note: adding --nproc=N can speedup the compilation step.

Note: you may need to use sudo depending on the permissions of your PHENIX installation.

Using the Git repository of cctbx.

To remain up-to-date with the changes in the cctbx project that contains many of the functions used in Q|R, remove the cctbx_project directory in the modules directory. The above command will clone it from GitHub.

manual qrefine installation

  cd $PHENIX
  git clone https://github.com/qrefine/qrefine.git modules/qrefine
  phenix.python -m pip install ase==3.17.0
  phenix.python -m pip install pymongo
  libtbx.configure qrefine

QM Interfaces

QR does not include the QM engines required to run optimization or refinement. You have to install them yourself.

Once you have installed them, you need to set an environment variable to allow QR to know where to find it. Below is a set of examples that give you and idea of how to get started, please modify the locations to match your own installation.

QM Code Example Setup for Bash Available at
ANI export NC_ROOT="/home/olexandr/notebooks/ASE_ANI" https://github.com/isayev/ASE_ANI
export LD_LIBRARY_PATH="$NC_ROOT/lib:$LD_LIBRARY_PATH"
export PYTHONPATH="$NC_ROOT/lib:$PYTHONPATH"
Gaussian export g16root=/opt/qmsoft/g16. http://gaussian.com/
. $g16root/g16/bsd/g16.profile
export PATH=$PATH:/opt/qmsoft/g16/bsd:/opt/qmsoft/g16/local
Mopac export MOPAC_COMMAND=/opt/mopac/MOPAC2016.exe http://openmopac.net/
Orca export Orca_COMMAND=/opt/qmsoft/orca/orca. https://orcaforum.kofo.mpg.de/app.php/portal
PyScf https://sunqm.github.io/pyscf/install.html
Terachem source /public/qmsoft/TeraChem/SetTCVars.sh http://www.petachem.com/
export TeraChem_COMMAND=/opt/qmsoft/tc/1.93/TeraChem/bin/terachem
Torchani https://github.com/aiqm/torchani
Turbomole http://www.turbomole.com/
xtb export XTBHOME=/home/qr/XTB https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/xtb
source XTB/Config_xtb_env.bash

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