Update doc for meeko v0.6.0

[rwxayheee]

Preview of the edited doc: https://rwxayheee-autodock-vina.readthedocs.io/en/latest/

Some updates are made to the existing tutorials to incorporate v0.6.0 changes in meeko.

In the following 3 tutorials:

• Basic docking
• Flexible docking
• Docking multiple ligands

There's some substantial rewrite so as to introduce new usage of receptor preparation with meeko and ligand preparation with scrubber in the last tutorial. The solution files are regenerated.

For the following 2 tutorials:

• Docking with zinc metalloproteins The receptor preparation part was edited but the rest is unchanged. However, the execution requires ADFR and an edited version of autogrid4 in ADFR.

• Hydrated docking This has some minor issue with current Meeko because the receptor happens to be a special case: https://github.com/forlilab/Meeko/issues/213 The tutorial has been updated in de97b1f. This includes some rewrite of receptor + ligand preparation. The results in solution were regenerated

The other 2 tutorials remained unchanged are:

• Docking with macrocycles The tutorial doesn't describe a specific example. But there're specific files in example/docking_with_macrocycles
• Python scripting This doesn't seem to need the update

Changes made to requirements

• Added gemmi for https://github.com/forlilab/Meeko/pull/206