31 March 98
by N.Guex
Energy
minimisation with CHARMm
To complete this tutorial, you need to download some material and install it on the Unix box where you run CHARMm. Then you need to download the pdb file 1APH (bovine insulin) that will be used as an example. As it contains two chains and three SS-bonds, it makes a reasonably complex example.
- Load the file 1APH.pdb (provided with
the tutorial
package)
- The most
important thing is to insure
that residues of each chain are numbered from 1 for each
chain. Otherwise CHARMm will be confused. In this
example, everything is fine. But just to be on the safe
side (and to learn how to proceed), select all residues
of chain A (simply click on one A in the control Panel)
and use the "Rename" item of the Edit menu. Type 1 in the
appropriate field and repeat the operation for the chain
B.
- Click in the label column of the
control panel in front of the Arg1. Go in the display
menu and set the label kind to "atom kind". Locate the
CZ.
- Select all residues contained in a
sphere of 10Å around the CZ of Arg22. To do so,
click on the "display around" icon in the main window
(the icon with a little circle). you will be prompted to
pick an atom. Pick the Arg22 CZ. A dialog appear. Choose
the "Select Groups that are within" radio button and type
10 in the radius field.
Some residues are selected. To visualise which ones, simply type several times on the enter key of the numeric keypad (PC users should use the + key of the numeric keypad). This will hide and display the selected residues.
- Use the "reset orientation" item of
the edit menu. (The protein might disappear from your
field of view do not panic!)
- Save a CHARMm Energy minimisation job
(file menu).
- The default settings will perform 200
cycles of energy minimisation with the steepest descent
method, followed by 200 steps by conjugate gradients,
followed by 200 steps by Newton-Rhapson.
- By default, an harmonic constraint of
2 is added on all CA to prevent them to move far away
from their initial location. The higher the constraint
the more the atoms will stay around their initial
position.
- To speed-up the tutorial, do only 100
steps of Newton-Rhapson minimisation and accept the
settings.
- Save the file under the name
"myjob.pdb"
- Transmit the file to your Unix
computation server in a new directory (the simplest way
is to use NFS, but if it is not available on your
computer, use ftp).
- Login on your remote computer and
type this command: Cmin myjob.pdb
- When the energy minimisation is done,
you will obtain several files:
myjob_E.pdb which contains the minimised coordinates and some information about the energy.
The other files can be useful to trace problems if the minimisation failed. If you don't want them, launch the minimisation with the command "Cmin -r myjob.pdb" and the script will do some clean-up.
- If you have moved the molecule while
the remote computer was computing, your file will not be
superposed if you load it directly. Therefore, use the
"reset orientation" item of the edit menu immediately
before loading the result.
- Get the file "myjob_E.pdb" by NFS or
FTP and load it in the viewer.
- As you can see, hydrogens capable of
H-bonding have been added. If you don't want them, use
the appropriate item of the edit menu to discard
them.
- Compare the two proteins and note that only the selected residues have moved. Note that the backbone of those residues has moved. As a supplementary exercise, repeat the same procedure but add a constrain of 0 (zero) to the the backbone in the energy minimisation dialog, and note that only the sidechains of the selected residues have moved.
Known caveats:
Only amino-acids are supported.
Nucleotides, solvent and HETATM are ignored but SS-bonds are
set-up correctly.
If you want to include some non-standard residues or chemical compounds, you will have to modify the Swiss-PdbViewer minimisation script and provide your own topologies files.