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   collaborators & acknowledgments

Tinker


14. Collaborators & Acknowledgments

The TINKER package has developed over a period of many years, very slowly during the late-1980's, and more rapidly since the mid 1990's in Jay Ponder's research group at the Washington University School of Medicine in St. Louis. Many people have played significant roles in the development of the package into its current form. The major contributors are listed below:

Stew Rubenstein
coordinate interconversions; original optimization methods and torsional angle manipulation

Craig Kundrot
molecular surface area & volume and their derivatives

Shawn Huston
original AMBER/OPLS implementation; free energy calculations; time correlation functions

Mike Dudek
DMA-derived multipole models for peptides and proteins

Yong "Mike" Kong
multipole electrostatics; dipole polarization; reaction field treatment; TINKER water model

Reece Hart
potential smoothing methodology; Scheraga's DEM, Straub's GDA and extensions

Mike Hodsdon
extension of the TINKER distgeom program and its application to NMR NOE structure determination

Rohit Pappu
potential smoothing methodology and PSS algorithms; rigid body optimization; GB/SA solvation derivatives

Wijnand Mooij
MM3 directional hydrogen bonding term; crystal lattice minimization code

Gerald Loeffler
stochastic/Langevin dynamics implementation

Marina Vorobieva
nucleic acid building module and parameter translation

Nina Sokolova

Peter Bagossi
TINKER force field parameters for alkanes and diatomics

Pengyu Ren
Ewald summation for polarizable atomic multipoles; TINKER force field for water, organics and peptides

Anders Carlsson
ligand field potential energy term for transition metals In addition, we would like to thank

Tom Darden
for making his particle mesh Ewald code generally available to the simulation community.
It is critically important that TINKER's distributed force field parameter sets exactly reproduce the intent of the original force field authors. We would like to thank Julian Tirado-Rives (OPLS-AA), Alex MacKerell (CHARMM22), and Adrian Roitberg and Carlos Simmerling (AMBER) for their help in testing TINKER's results against those given by the authentic programs and parameter sets. Lou Allinger has provided updated parameters for MM2 and MM3 on several occasions. His very successful methods provided the original inspiration for the development of TINKER.

Finally, we wish to thank the many users of the TINKER package for their suggestions and comments, praise and criticism, which have resulted in a variety of improvements.




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department of chemistry University of Cambridge