Use case: 4W52

[sgill2]

=== Attachment ===
Input:
4W52.pdb
SMILES.txt

Output:
Clusters[1-5].inpcrd/prmtop

=== Setup description ===

This is a workflow for docking diverse ligand poses and subsequently parameterizing/adding them to a protein system (T4 lysozyme) for simulation.

The lysozyme structures 4W52 was taken from the PDB. Non-Protein/water molecules were removed, and missing residues and hydrogens were added using ambertools14’s tleap.

Ligands were taken from the binder/nonbinder lists from the Shoichet lab’s website (http://www.bkslab.org/take-away.php). 120 ligand poses of each ligand were generated using OpenEye’s OMEGA2 (ver 2.5.1.4) program and then docked using OpenEye’s FRED (ver 3.2.0.2). The top scoring structure was used to initialize RMSD centroid clustering, taking the 5 most diverse clusters. The docked ligand structures were parameterized using ambertools14 (ver 15.06) antechamber with the AM1-BCC charge model, using the charges calculated from the most favorable docking pose for the rest of the ligand poses. Finally, the ligand and lysozyme structures were combined using tleap and parameterized with the GAFF and amber99SBILDN forcefields. TIP3PBOX waters were used with a box size of 10Å to the nearest protein residue. Counter Cl- ions were added using tleap’s addions2.