Open the 2ama file in chimera
command line: open 2ama
we will generate two set of atoms: one for the protein, one for the ligand. Then, you can run the autodock vina interface and analyse the results.
Let's start with the protein. First, remove all non necessary molecules:
delete solvent: del solvent
delete ions: del ions
delete ligand: del ligand
on the remaining molecule add the hydrogens.
save this first file so that you can work back on it in case something goes wrong:
menu file --> save mol2 and give a name i.e. receptor.mol2
o cl: write format mol2 #0 receptor.mol2 (#0 corresponds to the number of the model you want to save)
open back the 2ama file. Select the testosterone. To do so, do a CTRL + left click on any atom of the ligand. Once the atom selected (fluorescent green), press the up arrow. This will select all the atoms of the molecule.
then delete all the atoms that are not selected: del ~ sel
add the hydrogens: addh
Please, be careful. At this point it is crucial to check that the chemistry of the molecule has been correctly recognize (i.e. bond order). In case something's wrong, please use the molecule editor Tools --> Structure Editing --> Build structure. Remove the hydrogen (del element.H) and assign the correct type of atom if necessary.
! NB. the ~ symbol represents that not in chimera internal language. Learn to use it the most you can.
save the mol2 file of the ligand: write format mol2 #0 ligand.mol2
Now, you have two files with the molecules you need for the docking to proceed. Open them back to the chimera workspace (this time they will be two different models) and to finish the set up add the hydrogen atoms.
running the docking experiment.