when you add a file, or modify a file (on your local machine), to update the github repository
git add file_name
git commit -m "message here"
git push origin master
when you want to copy changes from the repo into your local machine
git pull
Loaded 5grn.pdb into Schrodinger and ran preparation (all default, except I deleted Cl atoms and remove waters with less than 1 H-bonds to non-waters, added missing side chains).
Saved file as 5grn_prepared.pdb.
Tasks -> Develop Pharmacophore Model, create pharmacophore model using -> Receptor-ligand complex
Import pdb 6T2W and prepare. Added missing side chains. Deleted SO4 ions. Remove waters with less than 1 H-bonds to non waters. Everything else default.
Saved file as 6t2w_prepared.pdb
Tasks -> Develop Pharmacophore Model, create pharmacophore model using -> Receptor-ligand complex