Analysing an active site


Building Loops


Building a functionnal unit from a monomer


Crystal Symmetries


Electron Density Maps


Energy minimisation


Fitting Residues into Electron Density


Homology modelling


Making Phi/Psi statistics


Superposing Proteins







Last modified
31 March 98
by N.Guex


Energy minimisation with AMBER

To complete this tutorial, you need to download some material and install it on the Unix box where you run AMBER. 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.

Step by Step

  • Load the file 1APH.pdb (provided with the tutorial package)

  • The most important thing is to insure that not two residues of each chain have the same number. Failure to assign unique residues numbers will prevent the "protonate" program of the AMBER suite to do a proper job, and the energy minimisation will fail.You must also insure that all residues are globally numbered consecutively (not restarting at 1 for each peptidic chain).

  • Select all residues with the appropriate item of the Select menu and then use the "Rename" item of the Edit menu. Type 1 in the "Renumber selected groups from" field. This will correct any numbering problem (except in the case where HETATM groups are present between amino-acids). Indeed HETATM groups are currently ignored as they need special topology files

  • Click in the label column of the control panel in front of the Arg22. 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 an AMBER Energy minimisation job (file menu).

  • The default settings will perform 200 cycles of energy minimisation. Only atoms of the selected residues will be allowed to move; other atoms will be taken into account during the minimisation but will remain at their initial position.

  • 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: "Amin myjob.pdb"
    If you have access to a parallel computer, you can launch the parallelized version of the sander minimisation module with the command "Amin -p 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 "Amin -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 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 use the "lock the backbone" option in the energy minimisation dialog, and note that only the sidechains of the selected residues have moved.

Known caveats:

This facility is provided only with the purpose of easing the energy minimisation set-up. 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. In any case, you are strongly advised to read the AMBER documentation.