Installation

Python3 (Anaconda)

Parmhess is written in Python3 and runs on Linux.

The easiest way to setup Python3 is to install Anaconda. It is freely available at https://www.anaconda.com/download/.

You should choose Anaconda for Linux (Python3.X), not Python2.7 nor for other operating system. Simply run bash Anaconda3-x.x.x-Linux-x86_64.sh to start the installation and follow the instruction. Root access is not necessary.

If you are an experienced Python3 user and prefer to use your own Python build, make sure that numpy and pyyaml be installed properly.

Gaussian 09 (G09)

QM and MM calculation is performed by Gaussian 09.

Any revision of G09 should work. However, there is a bug in G09 Rev. B.01 and thus special attention is needed in MK charge calculation. If you only have G09 B01, read the workaround in: http://ambermd.org/bugfixesat.html

AmberTools

AmberTools is used to identify the atom types and calculate RESP charges. After you have Anaconda installed, a simple command could be used to install a light version of AmberTools:

conda install ambertools -y -c http://ambermd.org/downloads/ambertools/conda/

Then, run antechamber and you should see the help of usage.

Parmhess

Download Parmhess from https://github.com/ruixingw/parmhess/releases

Extract the files to any folder. Create a soft-link to your $PATH. For example:

ln -s /PathToParmhess/parmhess.py ~/bin

Katachi

Download Katachi from https://github.com/ruixingw/katachi/releases.

Extract the files to any folder. Create a soft-link to your $PATH. For example:

ln -s /PathToKatachi/gokatachi.py ~/bin
ln -s /PathToKatachi/katachi.py ~/bin

Tsubasa

Download Tsubasa from https://github.com/ruixingw/tsubasa/releases Extract the files to any folder. Create a soft-link to your $PATH. For example:

ln -s /PathToTsubasa/tsubasa.py ~/bin