TINKER and AMOEBA
Tutorials for Tinker/AMOEBA MD simulations on CPU & GPU: CLICK HERE
GitHub site for software download: https://github.com/TinkerTools
Official AMOEBA parameters: CLICK HERE
Use POLTYPE for deriving new small ligands
Lab wikis:
Obsolete:
https://biomol.bme.utexas.edu/tinkergpu
Internal wiki: https://biomol.bme.utexas.edu/wiki
Lab cluster monitoring:
GPU cluster monitoring:
Server room temperature:
http://biomol.bme.utexas.edu/~pren/temper.htm
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