(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015

TUTORIAL B2 - SECTION 4

Using VMD with AMBER

By Ross Walker

Updated for VMD 1.9.2
[by Aditi Munshi and Ross Walker]

4) Loading AMBER inpcrd and restrt files

Let's remove the current molecule and try looking at an AMBER inpcrd or restrt file as created by xleap or sander. Start by removing the LADH molecule. Right click on the 1LDY.pdb file name in the "VMD Main" window and select "Delete Molecule". You may have to left click first to select it.

Next we will open a prmtop and inpcrd file I created with xleap. Don't worry about how these files were created. That will be covered in a later tutorial. Here are the two files you will need: TRPcage.prmtop, TRPcage.inpcrd.

Loading AMBER structures is slightly different to how you load a pdb file since there are actually two files. The first file is the prmtop or topology file. This says nothing about the locations of the atoms in a molecule‒it simply defines what each atom is, what it is bonded to, and the parameters for each atom type. The inpcrd file on the other hand simply lists a set of coordinates, but says nothing about the atoms. Thus we need both these files to load the structure. Lets start by looking at one of the limitations of the pdb view. Here is a pdb of this TRPcage structure I created using ambpdb. (TRPcage.pdb).

This structure I created by hand using xleap's sequence command, so it has some very poorly placed protons and residue side chains. Load the pdb into VMD and see what you get. It should look pretty good. However, try zooming in on the central Tryptophan residue. What do you see?

It might be easier to see what is going on if you remove the other residues. In "Graphical Representations" under "Selected Atoms" enter "all within 5 of resname TRP". This will only show atoms that are within 5 angstroms of residues called TRP. Also select CPK as the Drawing method while you are there. Next click on the Mouse menu in the "VMD Main" window and click "center". This allows us to change the center of rotation. Now click on the backbone nitrogen of the tryptophan. Now when you rotate it should rotate about this atom. (Press r to return to rotate mode).

What are those strange bonds? We have a proton with 3 bonds to it. Surely the simulation was not setup in this way. Indeed, it wasn't. But the pdb I created has no bond information in it. As such VMD added bonds based on the distance between atoms. Since this is a "very" bad starting structure there are a number of atoms very close together and so VMD bonded them all. Hence, looking at a pdb files does not tell you where the bonds that Amber will use are. In order to see how Amber will treat the bonding of this molecule we have to use the prmtop file.

So, delete this molecule so that we can load a prmtop instead. When loading AMBER prmtop files, it is important to know whether you have a new format prmtop file (created with AMBER7 or later) or an old one (created with AMBER 6 or earlier). The prmtop I gave you above is a NEW format. So, go to the Molecule File Browser and browse for the prmtop file. Now, under "Determine file type" select "parm7"[vmd1.8.3] or "AMBER 7 Parm"[vmd1.8.4 and newer].This indicates the NEW prmtop format (parm refers to the old format). Hit Load.

Not much happened right? That is because the prmtop file contains no coordinates. However it should have created a new structure container called "TRPcage.prmtop". We can now load any number of structures into this molecule by making sure it is selected in "Load files for:" in the Molecule File Browser.

Now we can load more or less any molecule format into this molecule. If we load our pdb file into this molecule we will get the same as before but this time the bonding will be that defined in the prmtop file. Try it. We can also load an inpcrd file (as created by LEaP) or a restrt file (as created by sander) into this molecule. To do this we browse for the file (TRPcage.inpcrd) and select "rst7"[vmd1.8.3] or "AMBER7 Restart"[vmd1.8.4] as the file type. Make sure TRPcage.prmtop is selected in the "Load files for:" box and then hit Load.

The bonding should look much better now. This is still too strained a structure, however, to be able to run MD so I have minimized it for you by using sander. Here is the restrt file from the end of the minimization. (TRPcage.rst).

We can load this as either a new molecule (by loading the prmtop file again) or as a new frame in the current molecule. I want to see the two molecules side by side so I will load it as a new molecule. So go to the "Molecule File Browser" window again and in the "Load files for:" box select "New Molecule". Now hit the Browse button and browse for the TRPcage.prmtop file. Select "AMBER7 Parm" as the type and hit Load. Now hit Browse again and find the TRPcage.rst file. Select "AMBER7 Restart" as the type and hit Load. You should now have two molecules displayed in the "OpenGL" window. They will be very similar. In order to see the difference between them lets color one of them in blue.

Go to the "Graphical Representation" window and under "Selected Molecule" select the first TRPcage.prmtop of the two in the list. This should be our initial (unminimized) structure. Then under Coloring Method choose "ColorID" and pick 0 in the box that appear to the right of it. You should see one of the molecules in the "OpenGL" window turn blue. You can now zoom in on this and look at the difference between the two structures.

As you might have guessed, the minimization has twisted the Tryptophan away from the backbone to avoid that really bad hydrogen contact we had. Can we calculate an RMSD for the minimization change? We could do this using AMBER's cpptraj command but we can also do it within VMD itself using the RMSD extension.


CLICK HERE TO GO TO SECTION 5


(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015