QM/MM calculations on thymine dimer repair.
DNA building
B (formely
know as Biomer) is a Java-based, on-line biomolecular modeling
package. It is useful for generating initial structures of biopolymers
and small organic molecules. We will use
B to create
double-stranded DNA oligomer. You are free to choose any sequence, as
long as there is at least one TT repeat on one of the strands. The
example files that we provide in this tutorial are based on a A20T20
oligomer.
Please consult the
B manual
and faq page for help on the model building. Save your DNA molecule in
pdb format. The pdb file of the A20T20 oligomer can be found
here.
Topology Building
To model the interactions we make use of the Amber99 forcefield. The
Amber port for gromacs can be downloaded from
Eric Sorin's webpage.
To allow the pdb2gmx tool to recognize the thymine dimer, we need to
modify the ffamber99.rtp residue database. We introduce two new
thymine residues dtA and dtB, and define additional interbase bonds
between the C5 atoms and the C6 atoms. Here is what your modified
ffamber99.rtp should look like.
With the pdb2gmx command we create the topology
(topol.top) and the configuration
(conf.gro):
localhost:~>pdb2gmx -ignh -f Bmodel.pdb
The -ignh flag ignores hydrogenatoms in the input file, and forces
pdb2gmx to construct the hydrogens based on the
ffamber99.hdb database.
We first perform a minimization in vacuum, using the steepest descent
algorithm. Check steep.mdp to
familiarize yourself with the minimization protocol that we follow.
We perform the minimization by executing grompp and then mdrun:
localhost:~>grompp -f steep.mdp
localhost:~>mdrun -v -c minimized.pdb
After minimization the DNA structure should looks like
this.
The next step is to add water and neutralize the system. We use the
gromacs tools editconf, genbox, and genion.
We first place the minimized structure in the center of a rectangular
box:
localhost:~>editconf -c -d 1.6 -f minimized.pdb -o boxed.pdb
Then, we add water, for which we use the tip4p model
localhost:~>genbox -cs tip4p.gro -cp boxed.pdb -p topol -o solved.pdb
Finally, we neutralize the overall negative charge of -38 by adding 38
sodium ions. We first need to create a tpr file, for which we use
neutralize.mdp:
localhost:~>grompp -f neutralize.mdp -c solved.pdb -p
topol
With the topol.tpr file, we can now use genion to place the 38
counter-ions at random positions in the box:
localhost:~>genion -np 38 -pname Na -o neutral.pdb
-random
We now have to modify the topology by adding 38 sodium ions (NA) and
removing 38 tip4p water molecules manually. The final topology file
can be found here. In what follows we
also need an index file that contain
the atomnumbers of the DNA, water and ions.
Equilibration
Because of possible overlap between water molecules and DNA atoms, we
have to minimize the model system. We use again the steepest descent
algortihm to remove possible strain in the initial structure. The mdp
file can be found here.
localhost:~>grompp -f mini_sol.mdp -p neutral.top -c
neutral.pdb -n neutral.ndx
localhost:~>mdrun -v -c neutral_mini.pdb
Then, we equilibrate the water and ions for 100 ps, using the
parameter in equi_sol.mdp. The heavy
atoms of the DNA are restrained during the
solvent equilibration.
localhost:~>grompp -f equi_sol.mdp -p neutral.top -c
neutral_mini.pdb -n neutral.ndx
localhost:~>mdrun -v -c neutral_sol_equi.pdb
The result of the solvent equilibration on the A20T20 oligomer is
available here.
updated 28/10/08
Next: II. Equilibration of the DNA
with gromacs Previous: Introduction