SIMONAPreprocessor
Flexscreen - First Steps

How to do your first molecule docking simulation.

This is just an example to get to know how this section works and what it does roughly. For more detailed information about all functions of POEM++ see here.

  • Get molecules
    In order to simulate a docking process you need an xml-datasheet. This sheet should be created by the SIMONA Preprocessor. The preprocessor needs two input files with the structures of molecules. A receptor and a ligand.
  • Startwindow
    Now start the SIMONA Preprocessor by typing
    1 python simonagui.py
    into the shell (you have to be in the directory where simonagui.py is located). In opening window you can choose of which type your simulation should be. Select Flexscreen for a docking simulation.

    2s_Mainpage.png

  • Input files
    In this step read in the *.mol2 files of the receptor and the ligand which you want to dock. Therefore select Configuration at the menu on the left hand side. Type the path of the input-files in the box beside Input receptor and Input ligand. You may also browse the paths by clicking the ... buttons beside the boxes. Also type the output-path in the box beside Output xml. To receive a file readable by SIMONA the file extension has to be *.xml.

    2s_Config_Input.png

  • Environment
    In this section the temperature has to be set. Temperature defines how free to move the molecules are. Either select Constant temperature or Geometric annealing. If constant temperature is selected only one temperature is to be entered in the box on the right. The temperature scale is in Kelvin. For a geometric annealed temperature a Start temperature and an End temperature are required. A standard simulation starts with a rather high, e.g. 500, while End temperature should be rather low, e.g. 5. But feel free to experiment with other settings.

    2s_Config_Envir.png

  • Simulation Settings
    For the outcome of a simulation the most important thing is the number of Simulation steps. The more you take, the better the result will be. But the needed calculation time will grow as well. Don't set more than 100.000 steps for your first try. Random seed should be selected.

    2s_Config_Settings.png

  • Forcefields
    Now we proceed to the next section of the left menu. Use the first four Forcefields for your simulation. Leave Scaling factors at 1.00

    2s_Forcefields.png

  • Moves
    In the third section of the side menu you have to define which moves your molecules should be able to do. Allow the Ligand Dihedral rotations , Rigid body translations and Rigid body rotations . Writing a * in the box beside Dihedral rotations enables all dihedral angles. Delta [A] should be set to 1.40 and Delta [°] should be set to 5.00

    2s_Moves_Ligand.png

    Usually the receptor is a huge protein, so limit its movement-possibilities to a minimum. A rigid body move is not necessary, because the ligand can move. Allow only the docking-pocket to move its dihedrals, therefore write the numbers of the dihedrals of the pocket into the box on the right. Another option to select a docking pocket is to write the relevant residues in the box on the bottom of the page. The format is:
    1 <number of the residue>.<amino acid (3-letter-code, upper case)>
    for example: 1234.LEU

    2s_Moves_Receptor.png

  • Output
    The fourth section of the side menu provides options for output settings. Select Std-, Trajectory- and Energy-output. Stepmod should be 1000 or more. The Output filename of the trajectory has to have the ending *.pdb or *.vcf. A *.vcf file contains coordinates only, so is smaller, but can't be read by visualization tools. A *.pdb file contains additional information, so can be easily visualized.

    2s_Output.png

  • Generate XML
    Last step on the way to your *.xml is to let the Preprocessor do its work. On the top menu select Generate XML and wait until the output file has been created. The output file will be saved at the position you selected earlier. It is shown in the side menu section Preprocessor output.

    2s_Prep.png

  • Start SIMONA
    So far you have created an input file for SIMONA. To run SIMONA with your molecule and your settings type
    1 poempp <outputfile.xml>
    in the shell. <outpufile.xml> is here the outputfile you created with SIMONA Preprocessor. Make sure you are in the right directory. SIMONA will start its work and after some time creates the requested files.
  • Result
    To see the outcome use a visualization tool. In the trajectory file you can see the evolution of the simulation. The last step of the calculation is saved in *_snap.pdb.