2.2.1 Dangers of PDB format for ligand input

2.2 Types of input ligands

Not all ligands can be successfully fit by flynn. Such types include large polypeptides or proteins, very flexible molecules, or simply molecules that contain atoms that the not present in the MMFF94s force-field.

Perhaps the most important property is rotatable bond count. Although flynn may be able to generate conformers for molecules with more than 20 rotatable bonds, the results of such an exercise would be dubious at best and should be taken with a grain of salt.

Flynn will automatically check for unhandled atom types, but will gladly try and fit large molecules or proteins that contain many rotatable bonds usually with dissapointing results.

2.2.1 Dangers of PDB format for ligand input

Many crystallography packages do not enforce writing out connection table or bond order information when outputting pdb files, or worse, strip them out. If bond distances are not correct flynn's attempt to automatically assign bond orders and atom types can be suspect. To facilitate this, flynn includes a -precheck flag that can be used to verify that the input ligand is identified correctly and for validation of the automatic bond order assignments.

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