Use Case: Chk1

[sgill2]

Setup Description

Chk1 with a bound fragment was prepared from a pharma derived dataset. The protein was prepared using pdbfixer to add missing residues and remove non-protein/ligand/water molecules. The protein was solvated using a 10 angstrom TIP3P box and 0.005M of Na+/Cl- counterions. Protein hydrogens were also added using pdbfixer at the crystallographic pH.
Because this pdb wasn't obtained from the PDB Database, it lacked a SEQRES, which pdbfixer uses to determine which residues to add, so the seqres from 1ia8 was manually inserted into the pdb.
The ligand lines from the pdb were removed and placed into it's own pdb, and Maestro was subsequently used to add missing ligand hydrogens. The ligand's charges were calculated using AM1-BCC. The protein and ligand pdbs were then combined using amber. Amber99SBILDN and GAFF were used as forcefields for the system.

Attachment

(Unfortunately I cannot share the files because of their origin.)