Some tips on installing AmberTools 16 together with Jupyter notebook

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AmberTools 16 together with Ipython notebook

Amber (starting from 16) supports Ipython notebook (also known as jupyther notebook), which is useful for trajectories visulization and analysis and is very powerful tool to record your commands.  Besides the amber mdcrd trajectories, you may also use it to analyze your gromacs trajectories. 

The strength of IPython notebook is that it is flexible and extendable and very user-friendly. 

In case you'd like to try IPython notebook together with MD trajectory analysis, you could first read few pages about Jupyter notebook and AMBER pytraj.


If you'd like to use it, these are useful step-by-step instructions for Pytraj with Ipython here :

You need to install conda or anaconda first. See this link  https://docs.continuum.io/anaconda/install


1. login to your remote server or local machine, and install ambertools16
do remember to enable --with-python
./configure --with-python=/path2conda/anaconda/2/bin/python

2. enable the AMBERHOME varible by typing the following in your terminal : 
$ export AMBERHOME=$HOME/software/amber16

3. set a virtual environment (named as amberAPI) for pytraj and cpptrj
$ conda create -n amberAPI  anaconda python=2.7
## you could change amberAPI to any other names as you like

4. enter into the virtual evironment named as amberAPI
$ source activate amberAPI
you will see this : 
(amberAPI)$[ john@localmachine ~ ]$

5. now install pytraj if you could not import pytraj directly
$ conda install pytraj -c ambermd
$ conda install ipython 
# if you'd like to use nglview 
$ conda install nglview -c ambermd

6. in order to use pytraj to visulize and analyze, you could login to nscc (through ntu.nscc.sg)
# set conda path if needed
$ export AMBERHOME=$HOME/software/amber16
$ source  activate amberAPI
## you will see a new environment 
(amberAPI)$[ john@localmachine ~ ]$
## you could exit the environment by source deactivate amberAPI

7. system has been configured,  enjoy your jupyter notebook now
go to your working directory, typing this in terminal
$ jupyter notebook



some commands here: 

any questions, just let me know.

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