Instructions
=========
Step 1.
Run Brownian dynamics simulations.
Copy necessary data and programs, to your local directory:
unzip /home/client1/data/sda.zip
or download and unzip the file sda.zip.
Chdir to sda/ directory and type:
>./bin/run_sda .
- in ~ 2 mins, this script will:
- compute electrostatic potentials of the proteins
using UHBD,
- prepare the necessary force field files,
- run BD simulations with SDA,
- write rate info to file "rates" (where the rate
of formation of 2 contacts at 7 A
is 3.7e9 M-1s-1, compared to the
experimental rate of 3e9 M-1s-1)
- write one trajectory to file fort.55,
- rewrite the trajectory to file cmxs200,
so that the trajectory snapshots are
separated in time by (approximately)
200 ps.
- convert this file to a standard format dynamics
trajectory file called cmxs.DCD
The computations performed are transparent if you look at the script
bin/run_sda. Parameter and input files all are in the data/ directory.
To understand exactly which parameters are used in the simulations,
you can look at the sda documentation which is accessible on the web
from
http://www-z.embl-heidelberg.de:8080/ExternalInfo/wade/pub/soft/SDA
Step 2.
Visualize a Brownian Dynamics simulation trajectory.
2a. Start vmd (type /home/client1/programs/vmd/vmd in a command prompt).
Stop rotation by pressing the left mouse
button.
2b. In the command-line window type: play vmd.in
- this will load 3 pdb files, colour them so that the target protein
(barnase) is blue, the moving protein (barstar) is red,
and the docked position
for barstar is green.
- The view will be adjusted by scaling and trajectory animation will
play once - this is the Brownian dynamics trajectory simulated.
2c. Click on the Animate button of the command window of vmd.
- You have the possibility to re-play the Brownian dynamics animation.
There are 5 buttons to manage animation: (from left to
right)
back_play - step_back - stop - step_forward - play_forward.
During the animation, you can alter the viewing perspective
as follows:
>to rotate, type 'r' and then press left-mouse
button;
>to scale, type 's' and then press left-mouse
button while moving the mouse
horizontally;
>to translate, type 't' then press left-mouse button.
- The time step between trajectory snapshots is 200 ps. During this
time
the proteins move ca. 6 A by random diffusion.
2d. At the beginning of the simulation, barstar is on the same side
of barnase as
its binding site, but its orientation
was not suitable for precise docking.
- Barstar then spent a lot of time (~50 ns) interacting with the guanine
binding loop of barnase, until it achieves the right orientation,
- Type in 261 in the Jump_To selection of the window animate to see
this.
- Then barstar moves away and comes back in ~15 ns, to adopt
an arrangement allowing subsequent docking
- Type in 337 in the Jump_To selection of the window animate to see
this arrangement.
2e. In Brownian dynamics simulations, association to formation of a
diffusional
encounter complex is simulated. The subsequent
step of docking to form
a fully bound complex is not simulated and
would require a more detailed
force field accounting for attractive short-range
interactions and side-chain
rearrangements. This means that after satisfaction
of contact criteria for
formation of a diffusional encounter complex
barstar eventually diffuses away
from barnase in the Brownian dynamics simulations.
- In this simulation, barstar remains in
close proximity to its docked position for ca 10 ns (steps
330-360),
which is significantly longer than side-chain rearrangement
times required for
docking of these proteins.