Notes

6cf2 - proteins
Centroids -
I came up with x number of structure (in lab methods)

there are three centroids in the folder that he sent us
the pdb file have been fixed already
Remove all of the sodiums from the centroids and the centroids will be the ligands in this experiment
Choose no torisons in auto dock
- one of the figure to have all centroids side by side
from the proteins, remove the RNA (by going into sequence and deleting them manually) and the heteromolecules like in the middle , salts, polar hygrogens and remove hydrogens in pymol and calciums and salts. Only want the amino acid proteins and pymol to remove all of the hydrogens and the polar hydrogens and remove all waters

Example of centroids - same RNA sequence
show the three centroids accquied with grey surface and that is one of the figures like in the previus reports
only do polar hydrogens in the receptor

receptor file - proteins with ligand centroid 1
protein with centroid 2
proteins with centroid 3
RNA is the ligand this time. It should be flipped

Torsions? No torisons on the ligands (centroids)
Which one to remove the polar hydrogens? Receptors

For the centroids remove salt and save as pdb and bring in to ligand into auto docks tool and select torsions and export into pdbqt

pymol - pdb - open into autodock - do the things - export into pdbqt