I’m writing this as how-to reference for installing useful software for MD research. I already wrote most of this a long time ago but is somewhere hidden in my GitHub, so I’m putting it here for easier access. Hopefully it’s also useful for someone else although this is all pretty much really basic and I decided write it down because I easily forget things.

Installing AmberTools

Follow Jason Swail’s guide.

In essence, these are the necessary things for AmberTools to work on a Mac:

  1. Instal Xcode

  2. Enable command-line tools

  3. Download macports

  4. Use macports to install the compilers for AmberTools to work

The gcc version 4.8 (known bug in here failed for me so I installed the 4.9 version. The commands were:

sudo port install gcc49
sudo port install mpich-gcc49
sudo port select --set gcc mp-gcc49
sudo port select --set mpi mpich-gcc49-fortran

Once you complete all of the above steps without errors, you can actually start the installation of AmberTools:

  1. Download them from here

  2. Follow the instructions in page 23 of the manual.

  • Everything worked for me using the most simple installation (./configure gnu)

If you do make test in your $AMBERHOME directory and everything is OK, you should see the following (after a lot of output):

All the tests PASSED
    1382 file comparisons passed
    0 file comparisons failed
    0 tests experienced errors
    Test log file saved as /usr/local/amber15/logs/test_at_serial/2015-10-28_15-26-42.log
No test diffs to save!

Installing VMD

Here are all of the downloadables.

I chose the latest version (1.9.2) and the MacOS X OpenGL (32-bit Intel x86) link.

A .dmg file is downloaded. Open it and then drag the VMD icon to the Applications folder. Done!

It won’t let you just open it yet: Apple blocks applications from non-verified distributors (a.k.a non-Apple) so you have to go to System Preferences > Security & Privacy and click on the General tab. There, click on the lower-left lock icon, and then select the Anywhere option under the Allow apps downloaded from: section. Now you can use vmd.

How to use vmd from the command line

Using VMD from the command line is very convenient as you can directly load the topology and trajectories files, or several PDBs very quickly. If you open VMD manually from the Dock it points every time to your home directory and you loose a lot of time manually navigating to wherever the files you want to visualize are.

  1. Remove the space from the name of the Application (i.e. VMD1.9.2). This is best done from the Finder (spaces in the command line are a pain to work with).

  2. Add this to your ~/.bash_profile file:

alias vmd='"$vmdappdir/Resources/VMD.app/Contents/MacOS/VMD" $*'

NOTE: VMD only has 32-bit version for Mac OS X. This is bad because you’ll only be able to open trajectories that are half the size of your RAM. More info on this issue here.

I’ve come up with a solution to this :heavy_exclamation_mark: Copy or download the script below and save it somewhere in your $PATH (for example, usr/local/bin). Then make it an executable with chmod +x load_big_trajs.sh.

# This script creates  a .tcl file in the /tmp/ directory
# with the necessary commands to call big trajectories
# from the command line. It uses a stride of 100 frames.
# If it still fails (memory error), change the stride to 
# a bigger number. The file in the /tmp/ directory is
# removed after vmd is closed. 

# Usage: load_big_trajs.sh topology.prmtop trajectories*.nc
if [[ $# -lt 2 ]]; then
    printf "Please provide at least two arguments (top and traj file)\n"
    printf "Usage: load_big_trajs.sh topology.prmtop trajectories*.nc\n"
    exit 1
tmpfile=$(mktemp /tmp/vmd_readin.tcl)
cat ~/Scripts/StateFile > $tmpfile # Comment this line out if you don't have a StateFile for VMD. Or change the path to were its sitting in your machine.
echo "mol new $prmtop" >> $tmpfile
for var in ${@:2} # We skip the first argument, the top file
    echo "mol addfile $var first 0 step $stride waitfor all" >> $tmpfile
/Applications/VMD1.9.2.app/Contents/Resources/VMD.app/Contents/MacOS/VMD -e $tmpfile -size 1920 1080
rm $tmpfile

Take a look at line 40 in the script and change the path to your VMD executable if it’s different! If you’ve followed the previous steps it should be the same as the one in the script, though. Now you’ll be able to load multiple trajectory files from the command line like so: load_big_trajs.sh topology.prmtop trajectories*.nc (provided you have a sensible naming scheme of your trajectories and they show up sequentially. Check this by doing ls trajectories*.nc).

My helpful screenshot

Installing UCSF Chimera

Here are all the downloadables.

Same procedure as VMD. Click on .dmg file, drag Chimera icon to the Applications folder.

The binary is in /Applications/Chimera.app/Contents/MacOS/chimera.

How to use chimera from the command line

Choose between:

  • Create an alias in your .bash_profile with alias chimera = '/Applications/Chimera.app/Contents/MacOS/chimera'
  • Do a symbolic link to somewhere in your $PATH with, for example:sudo ln -s /Applications/Chimera.app/Contents/MacOS/chimera /usr/local/bin/chimera

Either option should work. I think /usr/local/bin is in the default $PATH, check it by typing echo $PATH and looking for it. If not create it (with sudo) and append it to the $PATH in your ~/.bash_profile.