I am unable to generate parameter for iodide ion in tleap of amber. Amber parameter database doesn't have parameter for it. The force field I am using is ff99SB. Kindly suggest how I can go about it? Thanks a lot in advance.
First you need to construct the force field parameters with antechamber module available in amber package and then generate your files to run your simulation.
Ions are typically parametrized by computing their hydration free energies and comparing against experiments. There are many nuances to these calculations, such as choosing an appropriate reference state, accounting for surface tension effects, and making sure the box is large enough to avoid significant PME errors. The only adjustable parameters you have are the LJ epsilon and sigma, so that somewhat limits accuracy.
Is there any reference file or reference paper regarding manual parametrization? Justin Lemkul Martiniano Bello
This paper may be useful.
Chen, A. A., & Pappu, R. V. (2007). Parameters of monovalent ions in the AMBER-99 forcefield: Assessment of inaccuracies and proposed improvements. The Journal of Physical Chemistry B, 111(41), 11884-11887.
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