This page collects a list of instructions for installing and configuring applications which may be of use to scientists, students and engineers. Please add more...

See UbuntuScience for a list of applications.

How to install Latex

See LaTeX.

How to install TINKER (computational chemistry/biology)

TINKER, the fortran/java utility created by the Ponder lab at Washington University, St Louis, is distributed by that institution free of charge. It can recognize several formats of molecular structure files and can compute MD trajectories and inter- and intramolecular forces and the energies resulting from them. GUI and command-line are both available.

TO INSTALL TINKER: Visit the TINKER web site and download the installation kit. While you're there, fill out the license and read over the terms and conditions and get a copy of the user's manual.

Unpack the installation kit (I put mine in ~/Work/), it will create a file.

Run the installer script (change the permissions and then run the script by ./

That's it! I also made an alias in my .bashrc file where I added

alias tinker='/home/rajan/Work/tinker/ffe'

The difficulty comes if you are interested in working with molecules with more than 10000 atoms. In order to do this, you must recompile the suite of programs after you change the line       parameter (maxatm=10000) to read whatever you want the maximum number of atoms to be. This line is found in the file sizes.i, which is located in the source/ directory.

You must recompile the entire suite of programs because almost all of them refer to source/sizes.i

I did so by first copying the Makefile from make/Makefile to source/ and then altering the relevant information in that file. The alterations I made were: I took out the spaces around the = in the line TINKERDIR = /user/ponder/tinker and I changed the directory information to read /home/rajan/Work/tinker. The same changes are necessary with the next two lines.

Then I downloaded a compiler (g77-3.4 because it is easily available on synaptic). If you are also going to use the G77 compiler, you have to change the line       open (unit=iunit,file=name,status='old',position='append') to read       open (unit=iunit,file=name,status='old',access='append') in the openend.f file, also in source/.

You can recompile by hand, or use the make/Makefile that is provided. In order to use the Makefile, uncomment the correct lines for your system and recomment the one that has been uncommented, if necessary. The uncommented lines for me were:

F77 = /usr/intel/compiler70/ia32/bin/ifort


F77FLAGS = -c

OPTFLAGS = -O2 -cm -w

LIBFLAGS = -crusv


Then I recompiled and I had to move the files that were made upon compilation to the ../bin/ directory. This should have been done by the 'rename' section of the Makefile, but for some reason it wasn't. I cut out the commands from the 'rename' section and put them into a .sh script.

PM me (rajan) if you need any help with this.

Also, check out for another brief installation guide.

Tested on: [x] dapper [] edgy [] feisty

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Tested on: [] dapper [] edgy [] feisty

UbuntuScience/Howto (last edited 2017-09-16 20:43:04 by ckimes)