How to Install LigParGen Server Locally ?

I have many received many requests about making a local version of LigParGen server so that one doesn’t have to upload their ligand files to the web server. So we have made LigParGen python package that can be installed on Linux & Mac machines with anaconda python. Please follow the below steps to have a local version of LigParGen

  1. Install anaconda python
  2. Please request BOSS executable from Prof. William L. Jorgensen (It is free for academic users). Once you have BOSS, set $BOSSdir
  3. type `conda install -c mc-robinson ligpargen openbabel ` to install the package
  4. Download the files from here and copy them to $BOSSdir/scripts folder
  5. If this is done type “Converter -s ‘c1ccccc1’ -r BNZ -c 0 -o 0 -l” ,  this should generate BNZ.* in your tmp file. These are topology and parameters for Benzene in different force field formats.

Please email me if you have any questions at leela.dodda@yale.edu

Acknowledgements: Thank you, Matthew Robinson !! for Packaging LigParGen scripts.

Hope this makes your simulation setup a whole lot easier.

How to Install LigParGen Server Locally ?

The ORCA Quantum Chemistry Program

orca

ORCA is a free quantum chemistry software written by Prof. Frank Neese and cowokers. It has almost all the capabilities that are present in GAUSSIAN, GAMESS and NWChem. You can find the more info about ORCA at

http://www.mpibac.mpg.de/bac/logins/neese/description.php

This can also be run on PC’s and Laptops.

Check  the configuration of your Linux PC using

“uname -p ” command  if the answer is

i686 (download 32bit ) or i686 (download 64bit) from http://cec.mpg.de/forum/  by filling in the form

To run ORCA you need to have openmpi1.4.5 in your system so first install it as explained below (this is given in ORCA forums thanks to Reuti)

  •  tar xf openmpi-1.4.5.tar.gz
  •  mkdir my_openmpi
  •  cd my_openmpi
  •  ../openmpi-1.4.5/configure –prefix=$HOME/local/openmpi-1.4.5_gcc
  •  make
  • make install

Now Download ORCA  and

  • mkdir software
  • mv orca_2_9_1_linux_i686 software/
  • tar xf orca_2_9_1_linux_i686

After doing this go to home and add the following lines in .bashrc

  • export PATH=$HOME/local/openmpi-1.4.5_gcc/bin:$PATH
  • export LD_LIBRARY_PATH=$HOME/local/openmpi-.4.5_gcc/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}
  • alias orcaqm=’$HOME/software/orca_2_9_1_linux_i686/orca’

close the .bashrc file and do “exec bash”now test whether code is working or not by running following input file

%pal nprocs 8 end
 %MaxCore 3000
 ! RHF TightSCF PModel
 !opt

* xyz 0 1
 C 0.000000 0.000000 0.000000
 C 0.000000 0.000000 1.400000
 C 1.212436 0.000000 2.100000
 C 2.424871 0.000000 1.400000
 C 2.424871 0.000000 0.000000
 C 1.212436 0.000000 -0.700000
 H -0.943102 0.000000 1.944500
 H 1.212436 0.000000 3.189000
 H 3.367973 0.000000 1.944500
 H 3.367973 0.000000 -0.544500
 H 1.212436 0.000000 -1.789000
 H -0.943102 0.000000 -0.544500
 *

It runs very smoothly. Submit a job and go for a tea :)This procedure worked for me on my Lappy(Ubuntu), PC (Fedora) and on a small work station. If you have any problems leave a comment.

 

Aside