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README_INSTALL.MD

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Installation

Required Programs

  • Tinker, version >=8.9.4
  • GDMA, version 2.3 and greater
  • PSI4 (or Gaussian 09/16)

Required Tinker CPU Installation

git clone [email protected]:TinkerTools/Tinker.git tinker
cd tinker
cd fftw
./configure --prefix=/path_to_tinkerfolder/fftw/ --enable-openmp --enable-threads
make -j 8
make install
cd ..
cp ./make/Makefile ./source
cd source
  • Open Makefile and comment out default operating system (MAC, unless you have mac)
  • Uncomment the default linux installation lines
  • Keep the RENAME line commented out

Optional Tinker GPU Installation

  • Not required for parameterization purpose.
  • Install tinker CPU first.
git clone [email protected]:TinkerTools/tinker9.git
cd tinker9
cp -r TinkerCPU/* tinker/.
mkdir compile
cd compile
export CUDAHOME=/usr/local/cuda-10.2
export CUDACXX=$CUDAHOME/bin/nvcc
export FC=/usr/bin/gfortran
export CXX=/usr/bin/g++
export ACC=/home/liuchw/shared/nvidia/hpc_sdk/Linux_x86_64/21.1/compilers/bin/nvc++
export opt=release
export host=0
export prec=m
export compute_capability=80
export cuda_dir=$CUDAHOME
export CMAKEHOME=/home/liuchw/shared/cmake3.12/bin/
$CMAKEHOME/cmake ../
make -j

Python Envioronment

  • Simply using the following git command to download Poltype
git clone https://github.com/TinkerTools/poltype2.git master
  • Install anaconda
  • Use the following environment.yml file with conda env create -f environment.yml Source: #45 (comment)
  • Alternatively, you may use the provided environment.yml file (under Environments folder) to create a conda environment named "poltype"
  • environment.yml:
name: mypoltype2
channels:
  - conda-forge
  - rdkit
  - salilab
dependencies:
  - micromamba
  - psi4
  - geometric
  - mdanalysis
  - openbabel
  - svgutils
  - cairosvg
  - psutil
  - mdtraj
  - openpyxl
  - pdb2pqr
  - pdbfixer
  - rdkit
  - modeller
  - gdma
  - pip
  - pip:
    - pymbar
    - PyAstronomy
    - ase 
    - jax
  • Download GDMA-2.3 and greater
  • Note do not put source in your default .bashrc profile
  • Note do not keep multiple sources for different purposes (unless necessary) in the same .bashrc source file, this can cause internal conflicts to arise

Install fennol

git clone https://github.com/thomasple/FeNNol.git
cd FeNNol
pip install .

Optional explicit Conda Installation

  • Only do this if the above .yml file doesnt work
conda create --name amoebamdpoltype -c psi4 psi4 --yes
conda install -c conda-forge geometric --yes
conda activate amoebamdpoltype
conda config --add channels conda-forge
conda install mdanalysis --yes
conda install -c conda-forge openbabel --yes
conda install -c rdkit rdkit --yes
pip install PyAstronomy
conda install -c conda-forge svgutils --yes
conda install -c conda-forge cairosvg --yes
conda install -c conda-forge psutil --yes
conda install -c conda-forge mdtraj --yes
conda install -c conda-forge pymbar --yes
conda install -c salilab modeller --yes
conda install -c anaconda openpyxl --yes
conda install -c conda-forge pdb2pqr --yes
conda install -c conda-forge pdbfixer --yes

Required explicit Conda Installation - XTB

conda create --name xtbenv
conda activate xtbenv
conda install -c conda-forge xtb --yes
  • add the path to xtb binary in PATH

Explicit Conda Installation - ANI

conda install -c conda-forge ase --yes
conda install -c conda-forge torchani --yes
conda install -c conda-forge openbabel --yes
  • Install via ani.yml file (under Environments)

Environment var for running POLTYPE:

Create environments for Tinker,Gaussian 09,and GDMA. Put these in a file and source it before running POLTYPE so that programs such as "analyze.x" "gdma" "g16" can be found. You can use "which" to verify.

  • Example bashrc that you should source before running poltype. Note "mypoltype2" matches the conda env above
export myusername=`whoami`
conda activate mypoltype2
export g09root=/opt/g09gh/gaussian
source $g09root/g09/bsd/g09.profile
export GAUSS_SCRDIR=/scratch/$myusername/
export GDMADIR=/opt/gdma/gdma-2.3.3/bin/
export PATH=/opt/gdma/gdma-2.3.3/bin/:$PATH
export PSI_SCRATCH=/scratch/$myusername/
# add tinker exe to path