Software & Databases

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:

http://biomol.bme.utexas.edu/tinkergpu/