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.
Preprocessor. The preprocessor needs two input files with the structures of molecules. A receptor and a ligand.
SIMONAPreprocessor by typing
simonagui.pyis located). In opening window you can choose of which type your simulation should be. Select
Flexscreenfor a docking simulation.
Configurationat the menu on the left hand side. Type the path of the input-files in the box beside
ligand. You may also browse the paths by clicking the
... buttons beside the boxes. Also type the output-path in the box beside
xml. To receive a file readable by
SIMONAthe file extension has to be *.xml.
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
temperatureare required. A standard simulation starts with a rather high, e.g. 500, while
temperatureshould be rather low, e.g. 5. But feel free to experiment with other settings.
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.
seedshould be selected.
rotations. Writing a * in the box beside
rotationsenables all dihedral angles. Delta [A] should be set to 1.40 and Delta [°] should be set to 5.00
Stepmodshould be 1000 or more. The
filenameof 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.
Preprocessordo its work. On the top menu select
XMLand 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. Make sure you are in the right directory. SIMONA will start its work and after some time creates the requested files.