The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases.

The TINKER package includes a variety of novel algorithms such as a flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, a selection of continuum solvation treatments including several variants of the generalized Born (GB/SA) model, the generalized Kirkwood implicit solvation model for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, an efficient truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, velocity Verlet stochastic dynamics, use of pairwise neighbor lists or improved spherical energy cutoff methods, particle mesh Ewald summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, a new distance geometry metrization method that has greater speed and better sampling than standard methods, Elber's reaction path methods, our potential smoothing and search (PSS) methods for global optimization, an efficient potential surface scanning procedure, and more....