How?

• remove old versions

rm -rf $AMBERHOME/lib/python2.7/site-packages/pytraj
# you might need to change to your python version
rm -rf $AMBERHOME/lib/libcpptraj.so # or libcpptraj.dylib if using osx

• install pytraj

Either using conda (prefer) or using pip

conda

amber.conda install -c ambermd pytraj==1.0.7

pip

amber.pip install pytraj --prefix=$AMBERHOME --upgrade

• check

# get version
amber.python -c 'import pytraj; print(pytraj.__version__)'

# get pytraj directory
amber.python -c 'import pytraj; print(pytraj)'

Notes

If getting amber.python: command not found, try with normal python command. Please check Amber16 manual.