Molecular Dynamics and Drug Selection

I wanted a selection of drugs in my database, those commonly used such as aspirin , those currently used for myeloma such as lenalidomide, those suggested for the future for myeloma such as JQ1, and those I feel comfortable at trying which have been taken by humanity for centuries and derived from fruits, spices, herbs etc.  For all the drugs we need a PDB file.  You might be able to find it at the RCSB PDB site but you will be able to do so at the  Pubchem site.  Search for aspirin and you will find it , select it and the page displays the detail with a "Download" button.  Select the 2D structure and download the SDF file.  If you open it with a text editor it displays the locations of the atoms in its construction.  If you drag it into the VegaZZ program it displays the construction. Try "View" , "label" , "element" and you can see the detail molecular construction.  Rotating it you will see it is a flat representation which does NOT display actual shape.

Use edit, add, cluster, water say size 20 to "place the molecule into water2.  Then calculate , ammp, minimisation  and the molecule begins to take some shape.  Save this as a PDB ( 2.2) file, say asp.pdb.  If you open that file in a text editor you can see the various atoms of its contruction with their 3 dimensional x,y,z coordinates.
Now we have a PDB file and can load it into Autodock Tools.  Here again display, label, atoms  shows the construction.  This program prepares the molecule data to be used in a docking simulation.  As this is a drug it is classed as a "ligand". So ligand, input, choose , the asp we have loaded and charges are added, flexible bonds identified etc , ready for docking.  ligand , output , save as pdbqt gives you the file asp.pdbqt in the location of your choice.

This needs to be done for each and every drug you wish to run test simulations for.

I guess I have a hundred or so now by selection of active molecules from turmeric, green tea, milk thistle, raspberries, apples  etc etc.

If you can get to the same position with curcumin then in Autodock Tools it will look like this.

Curcumin ligand