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
The FreeformSolvNoSym method can be calculated with:
freeform -calc solv -solvcharges am1bccNoSymSPt -ionic uncharged
The workflow for OmegaZap using mostly command line tools from OpenEye is as follows:
omega2 -maxconfs 1 -sampleH true