Prime User Manual - ISP

52
Chapter 7: Prime–Refinement
For all kinds of structures, the following condition must be met:
• The structure must be an all-atom structure.
This condition applies to the protein and any ligand, waters or cofactors present in the
structure: all hydrogens must be present.
You can add hydrogens to a structure by displaying the structure in the Workspace and
double-clicking the Add hydrogens button in the toolbar.
However, for structures containing nonstandard residues, you must correct bond orders
and formal charges first.
For structures with nonstandard residues, the following conditions must be met:
• No residue can consist of disconnected pieces without formal bonds.
This means, among other things, that metals should not have formal bonds to the rest of
the structure, and should be treated as ionic. For example, in hemes the Fe must be a separate
residue with a +2 formal charge and no bonds, and the “bonded” N atoms must have
a –1 formal charge.
• Bound residues must contain at least 3 atoms between bonds to other residues.
This means that, for example, a dihedral angle cannot span more than 2 residues.
• Bond orders and formal charges must be corrected.
For nonstandard residues the supplied structure will be used, and you must check for correct
bond orders and formal charges.
When you rename residues, you should be aware that OPLS_2005 parameters are used for
standard residues and nonstandard residues.
Proteins can also be used as ligands, and the same conditions apply. No special treatment is
needed for two distinct chains connected by a disulfide or similar side-chain linkage. If the
“ligand” chain has nonstandard terminal groups or is connected to the main chain by its backbone,
two steps are required to make sure that the “ligand” chain is treated correctly:
1. Rename standard residues appearing in the ligand to nonstandard names.
2. Rename the atoms in inter-residue C–N bonds between renamed (ligand) residues. For
example, change “_C__ “to “_C*_”, where the underscores represent spaces. Other
atoms can keep their PDB names; only one of C or N needs to be changed.
Prime 2.1 User Manual