Loading coordinate files into VMD with the help of an AMBER topology file

AMBER topology files have a lot more information in them than simple .pdbs so sometimes it's really useful to be able to load them in directly, for example when you want to look at atomic charges. It is pretty easy to load AMBER files into Pymol using the load command. If you have prmtop and inpcrd/rst files form AMBGMIN/A9OPTIM - you can load them as follows:

1. Rename your example.prmtop file -> example.top (needed as Pymol doesn't recognise the .prmtop extension as being an AMBER file)
2. if using a *.inpcrd file, rename it as *.rst (same reason as above)
3. load the topology file (example.top) into an object (called mol in this example), then load the coordinate (example.rst) file into the same object

load example.top,mol
load example.rst,mol

Done! You can of course load multiple sets of coordinates into this object by repeating the second command. Now you've got it loaded, you can for example colour the atoms by the partial charge (as that information is in the AMBER topology file) using a command like this:

cmd.spectrum("pc", "blue_white_red", "all")