AMOEBA PARAMETERS
Tutorials for using Tinker and Tinker-OpenMM for MD simulations on CPU & GPU: CLICK HERE
Official AMOEBA parameters: CLICK HERE
Use POLTYPE for new small ligands
SAPT ENERGY DECOMPOSITION DATABASE FOR ORGANIC MOLECULES, PROTEIN SIDE CHAIN ANALOGS
https://biomol.bme.utexas.edu/~SAPT/sapt_database/
“General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field,” Qiantao Wang, Joshua A. Rackers, Chenfeng He, Rui Qi, Christophe Narth, Louis Lagardere, Nohad Gresh, Jay W. Ponder, Jean-Philip Piquemal , and Pengyu Ren J. Chem. Theory Comput., 2015, 11 (6), pp 2609–2618
SAPT VDW COMPONENTS
Additional test set discussed in paper:http://biomol.bme.utexas.edu/~ch38988/s36x7/
General van der Waals potential for common organic molecules, Rui Qi, Qiantao Wang, Pengyu Ren (2016), , Bioorganic & Medicinal Chemistry. http://dx.doi.org/10.1016/j.bmc.2016.07.062
RUNNING TINKER/AMOEBA MOLECULAR DYNAMICS on GPU
Running Molecular Dynamics using TINKER inputs and OpenMM engine through TINKER-OpenMM interface: