03_Anaconda_and_Related_Packages_Installations.md

Creating Anaconda Environment and Installing Tools

Important Conda Channels

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels ambermd
conda config --add channels rdkit
conda config --add channels salilab

Creating Conda Environment

conda create --name <env_name> python=3.x
conda activate <env_name>

Installing Packages

NGLView

pip install nglview
jupyter-nbextension enable --py --user widgetsnbextension
jupyter-nbextension enable --py --user nglview

BioBB

conda install -c bioconda biobb_analysis
conda install -c bioconda biobb_io
conda install -c bioconda biobb_model
conda install -c bioconda biobb_md
conda install -c bioconda biobb_chemistry
conda install -c bioconda biobb_structure_utils

Gromacs

conda install -c bioconda gromacs

AmberTools

conda install -c conda-forge ambertools
conda update -c conda-forge ambertools

RDkit

conda install -c rdkit rdkit

Modeller

conda install -c salilab modeller

PyRama

pip install pyrama

OpenMM

conda install -c omnia openmm

or

conda install -c conda-forge openmm

or with GPU support

conda install -c conda-forge openmm cudatoolkit=10.1

NAMD

conda install -c cbarnett namd

MDtraj

conda install -c conda-forge mdtraj

Pytraj

conda install -c ambermd pytraj

MDAnalysis

conda install -c conda-forge mdanalysis

EvoQSAR

conda install -c r r-qsardata

rQSAR

conda install -c geneko evoqsar

R

conda install -c r r