MDFF with Domain Restraints

This section will show you how to set up MDFF simulations with domain restraints in vaccum. Domain restraints apply harmonic forces to user defined groups of atoms to maintain a rigid domain during MDFF simulations.

Preparing the initial structure

For this example we will be using a protein called Acetyl CoA Synthase, found in acoasyn-initial.pdb. The structure has already been rigid-body docked to a simulated density map of the protein in a different conformation. Refer to the section 2 for information on generating a simulated density map and rigid-body docking. You will also need to create a psf file following the same steps outlined there using the acoasyn-initial.pdb model.

1

Start a new VMD session.

2

Load the initial structure in VMD by typing:

mol new acoasyn-initial.pdb

3

Use the AutoPSF plugin as in Section 2.1. If you are working on the same VMD session from the beginning of the tutorial, make sure you click the Reset AutoPSF button and the choose the correct molecule in the AutoPSF plugin. Follow the same steps as before to make acoasyn-initial_autopsf.psf and acoasyn-initial_autopsf.pdb.

4

Generate a PDB file containing the per-atom scaling factors $w_j$ in Equation 1, as in the previous section.

mdff gridpdb -psf acoasyn-initial_autopsf.psf -pdb acoasyn-initial_autopsf.pdb
-o acoasyn-grid.pdb

5

Generate secondary structure restraints as in the previous section:

package require ssrestraints
ssrestraints -psf acoasyn-initial_autopsf.psf -pdb acoasyn-initial_autopsf.pdb
-o acoasyn-extrabonds.txt -hbonds

6

Generate restraints to prevent cis/trans peptide transitions and chirality errors:

mol new acoasyn-initial_autopsf.psf
mol addfile acoasyn-initial_autopsf.pdb
cispeptide restrain -o acoasyn-extrabonds-cispeptide.txt
chirality restrain -o acoasyn-extrabonds-chirality.txt

Setting up the Domain PDB file

In order to define the domains that will be restrained, we must make a PDB file conaining our designations. Domain restraints based on the Targeted MD (TMD) function of NAMD, so we will be setting up our restraints as a TMD run. For more information on TMD please read the NAMD documentation.

1

Load the pdb file we are using for the initial structure

mol new acoasyn-initial_autopsf.psf
mol addfile acoasyn-initial_autopsf.pdb

2

Select each group of atoms and set their beta column to the proper domain designation

set sel [atomselect top "all"]
$sel set beta 0
$sel set occupancy 0
set sel1 [atomselect top "segname 1 and name CA"]
$sel1 set beta 1
$sel1 set occupancy 1
set sel2 [atomselect top "segname 2 and name CA"]
$sel2 set beta 2
$sel2 set occupancy 1
$sel writepdb domain.pdb

Placing a 1 in the occupancy column lets NAMD know that these atoms should be involved in TMD. Atoms with the same beta value (>0) are treated as a single domain. Here we have assigned two domains (beta 1 and 2) which will be kept rigid during the MDFF simulations. These domains are shown using VMD in Fig. 11.

Figure 11: The two domains defined by the pdb file. Domain 1 in red and domain 2 in blue.

Running the MDFF simulation

Generate NAMD configuration files similarly to the first example. We will be using the density map provided, acoasyn-target.dx. For information regarding generating simulated density maps, please see the first MDFF tutorial section  2.

1

Generate a NAMD configuration file:

mdff setup -o domain -psf acoasyn-initial_autopsf.psf
-pdb acoasyn-initial_autopsf.pdb
-griddx acoasyn-target.dx
-gridpdb acoasyn-grid.pdb
-extrab {acoasyn-extrabonds.txt acoasyn-extrabonds-cispeptide.txt
acoasyn-extrabonds-chirality.txt} -gscale 1.0 -minsteps 2000
-numsteps 70000

2

Now we need to edit the configuration file domain-step1.namd that we just created by adding in the TMD parameters necessary for domain restraints. Open the file in any text editor and add the following lines anywhere:

tmd on
tmdfile domain.pdb
tmdk 500.
tmdfirststep 2001
tmdlaststep 72000
tmdoutputfreq 1000

These parameters turn TMD on and let NAMD know where to look for the domain information. tmdk is a constant which scales the harmonic force applied by the restraint on a domain and this constant is scaled down by the number of atoms in a domain. One can specify a per-atom force constant that assign force constant to individual atoms which is not discussed here. More information about these parameters can be found in the TMD documentation in the NAMD User's Guide.

3

Quit VMD.

4

Run NAMD using the configuration file generated by VMD, i.e., run the following command in a terminal:

namd2 domain-step1.namd > domain-step1.log

This step should take about 1.5 hours on a single desktop processor core. If you don't want to wait, you can proceed to the next step and use the provided trajectory files, as explained in the next section.

Analyzing the results

The resulting trajectory will be saved to the file domain-step1.dcd. If you want to continue working through the tutorial before the simulation is complete, you can use the provided trajectory file domain-step1-result.dcd instead. As in the previous sections, load the trajectory files and target structure acoasyn-target.pdb into VMD and repeat the RMSD and CCC analysis. Now try running the same simulation without any restraints by turning Targeted MD off by switching tmd on in the configuration file to tmd off and changing the output name to no-domain. Again, you can continue the tutorial by using the provided trajectory no-domain-step1-result.dcd. Load the trajectory and target structure into VMD and repeat the RMSD and CCC analysis. Also, look at the trajectories and comparing the cases with and without restraints.