TINKER-OPENMM:Amoeba

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AMOEBA library

Official AMOEBA parameters are distributed with Tinker: https://github.com/jayponder/tinker/params/:

For new small molecules

Recent updates & next-gen development

  • Halegen compounds (2014): Mu et al, JPCB 2014, 118 (24), pp 6456. Not yet in official release of small molecule params.
  • Mg, Ca ions (2017): minor update included in ameobapro13.prm in summer 2017
  • SAPT database between organic molecules, protein side chain analogs
      http://biomol.bme.utexas.edu/~ch38988/s101x7 [1]
  • 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
  • General van der Waals potential for common organic molecules, Rui Qi, Qiantao Wang, Pengyu Ren (2016) Bioorganic & Medicinal Chemistry, 24, 4911–4919
  • Capturing Many-body Interactions with Classical Dipole Induction Models, C Liu, R Qi, Q Wang, JP Piquemal, P Ren, Journal of Chemical Theory and Computation 2017, 13 (6), 2751–2761



ForceBalance

Installation

  • ForceBalance can be installed easily, only if your local python settings are proper. Otherwise, I recommend you to install a fresh python 2.7  
  • Install Python 2.7.14
    • Download the 2.7.14 compressed file from python website; release the file then do the following 
      • cd ...../Python-2.7.14/
      • ./configure --prefix=/your/local/directory
      • make
      • make install
      • After installation, add the prefix to your $PATH environmental variable
    • Install the required python modules: numpy v1.5, scipy v0.9 (scipy depends on numpy, so install numpy first), lxml (if you want to use OpenMM interface, otherwise you can ignore this)
      • Exactly the same commands are used:  {python setup.py build} then {python setup.py install}
      • If other modules are also needed, I recommend git clone the modules then use the above two commands to install
  • Install ForceBalance
    • git clone https://github.com/leeping/forcebalance (this will clone the whole FB files to your $currentworkingdirectory)
    • cd ...../forcebalance
    • python setup.py build (note that if --prefix is not specified, forcebalance module will appear in your python site-packages) 
    • python setup.py install
    • Note that python does not always recognize the modules in the custom location. You may need to explicitly set $PYTHONPATH to the location where the modules are.
  • Run a case to test your installation (in forcebalance/studies/ choose one to run.  Note that if you want to run with TINKER, you need to set the tinker_path)

References and citations

Ren, P. and J.W. Ponder, Polarizable atomic multipole water model for molecular mechanics simulation. The Journal of Physical Chemistry B, 2003. 107(24): p. 5933-5947.

Ponder, J.W., C. Wu, P. Ren, V.S. Pande, J.D. Chodera, M.J. Schnieders, I. Haque, D.L. Mobley, D.S. Lambrecht, and R.A. DiStasio Jr, Current status of the AMOEBA polarizable force field. The journal of physical chemistry B, 2010. 114(8): p. 2549-2564.

Ren, P., C. Wu, and J.W. Ponder, Polarizable atomic multipole-based molecular mechanics for organic molecules. Journal of chemical theory and computation, 2011. 7(10): p. 3143-3161.

Wu, J.C., G. Chattree, and P. Ren, Automation of AMOEBA polarizable force field parameterization for small molecules. Theoretical chemistry accounts, 2012. 131(3): p. 1138.

Shi, Y., Z. Xia, J. Zhang, R. Best, C. Wu, J.W. Ponder, and P. Ren, Polarizable atomic multipole-based AMOEBA force field for proteins. Journal of chemical theory and computation, 2013. 9(9): p. 4046-4063.