Efficient Calculation of SAMPL4 Hydration Free Energies Using OMEGA, SZYBKI, QUACPAC, and Zap TK

Benjamin A. Ellingson, Matthew T. Geballe, Stanislaw Wlodek, Christopher I. Bayly, A. Geoffrey Skillman, and Anthony Nicholls

All authors:
OpenEye Scientific Sofware, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA

Corresponding author:
B. A. Ellingson
e-mail: ben@eyesopen.com
phone: (505) 473-7385 x90



A CSV file, All_Methods_SAMPL4, containing for all of our submitted data is available in supporting information.

The FreeformSolv methods discussed in the paper were calculated using the freeform utility, which is available in the SZYBKI 1.8.0 package.  The submissions were calculated with a pre-release beta version of freeform, so results with version 1.8.0 may differ.  The FreeformSolv method can be calculated with: 

freeform -calc solv -solvcharges am1bccSymSPt -ionic uncharged <input> 

The FreeformSolvNoSym method can be calculated with: 

freeform -calc solv -solvcharges am1bccNoSymSPt -ionic uncharged <input>

The workflow for OmegaZap using mostly command line tools from OpenEye is as follows:

omega2 -maxconfs 1 -sampleH true <input> <output>
szybki <input> <output>
molcharge -method am1bcc <input> <output>
zap9_transfer.py <input>

This workflow assumes that the OpenEye applications are in the PATH.  The hydration free energy is calculated using zap9_transfer.py, which is available in supporting information.