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6 Sampling Configuration Space

(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 2010

6.6 Nudged Elastic Band (NEB) simulations - SECTION 3

By Christina Bergonzo, Carlos Simmerling & Ross Walker

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3. Creating the NEB prmtop and inpcrd files

We now need to create a series of replicates (in this case an additional 30 giving a total of 32 structures with the current end points that we already have) that will stretch along our pathway and all be joined by springs. Ideally, so as to require the least amount of equilibration time, we should place these structures evenly along what we think is the best pathway. Lets for the moment though assume that we have no idea what the pathway looks like. In this situation what do we do? The simplest solution is to place half of the structures on one end point and half on the other. We can then carry out simulated annealing on the system and the spring forces between the structures will cause then to stretch out along the pathway. Thus the NEB method should locate the pathway for us. This is the beauty of the simulated annealing approach to NEB implemented in AMBER 11. You don't necessarily need to provide an initial guess of the pathway. The situation where the distance between images (spring extension) is zero is explicitly handled in the code so that you do not obtain infinite spring forces on the first step.

In order to create our prmtop and inpcrd files we will use tleap to build endpoint prmtop and coordinate files, and use the multisander functionality to run our NEB simulations.

In our case we will use a single prmtop file for our molecule, since the topology is the same everywhere along the pathway, including the two inpcrd files representing the two pathway endpoints. These we will generate from the struct1.pdb and struct2.pdb files from the previous section.

The first stage is to create the prmtop file and the two inpcrd files. These will be regular prmtop and inpcrd files and we shall create them using tleap the command line version of Leap. This is the point at which we decide which force field/parameters etc that we will be using since the parameters in the single image prmtop file we create will be the ones used in the NEB simulation. For this tutorial we shall be using the FF03 force field. Make sure the AMBERHOME environment variable points to the amber11 installation and that $AMBERHOME/exe is in your path. Then fire up tleap:

tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB

This will start up tleap with the ff99SB force field. If we had any non-standard residues in our system now would be the time load any mol2 files, frcmod files etc. Next we enter the following commands into the tleap terminal to create the prmtop and inpcrd files:

str1=loadpdb struct1.pdb
str2=loadpdb struct2.pdb
saveamberparm str1 str1.prmtop str1.inpcrd
saveamberparm str2 str2.prmtop str2.inpcrd

Input Files: struct1.pdb, struct2.pdb
Output Files: str1.prmtop, str1.inpcrd, str2.prmtop, str2.inpcrd

The first thing that you should check here is that the two prmtop files are identical:

diff str1.prmtop str2.prmtop

This should return no differences with the exception of the line specifying the creation time. Since our two end points are the same molecule, just in different conformations, it is essential that the two prmtop files be identical. In fact this is a requirement for NEB to work. Since the prmtops are identical we can discard one of them. In this case we will keep str1.prmtop and use that from now on. At this point it is probably a good idea to make a quick visual check of the two end points using VMD. Load the str1.prmtop file and then load each of the two inpcrd files (selecting rst7 [vmd 1.8.3] or amber7 restart [vmd 1.8.4 or later] as the file type). You should then have a two frame view where you can flip between the two end points. You should check that this is what you expect. I find such visual checks are always good as they can save you from wasting a lot of time (both human and computer) and effort trying to simulate something you didn't intend to. So, if everything looks good the next step is to use these files in an NEB compatible way.

Now we have the NEB prmtop and inpcrd files prepared, and we are ready to proceed to the next stage where we will run NEB MD and slowly heat the system up.