Computational Drug Discovery and Design

into account [33]. A symmetry correction applies when: (a) the

ligand is symmetric or contains a symmetric moiety; (b) the

equivalent (symmetric) orientations or the ligand are not sam-

pled during the simulations, typically due to large energy bar-

riers between the orientations; and (c) the restraints used break

the symmetry, such that the normally equivalent orientations of

the molecule have different energies due to the biasing poten-

tial employed [33]. For a ligand with a numberσLof symmetric

and thus equivalent orientations, this correction amounts to

ΔGsym¼kTln(σL). Thus, at 300 K, for a benzene molecule

ΔGsym¼kTln(12)¼ 1 .48 kcal/mol;while for a ligand

containing a phenyl groupΔGsym¼kTln(2)¼ 0 .41 kcal/

mol.

10. Thealchemical_analysis.pyscript may be run as follows:

alchemical_analysis.py –d dhdl_files/ –s 1000 –t 298 –w –g

Where the--dflag specifies the directory containing the

files with the∂U/∂λandΔUijinformation from all the win-

dows; the--sflag specifies the amount of simulation time

(in ps) to discard as equilibration period;t specifies the

temperature in Kelvin;wasks for the overlap matrix to be

plotted; and--g asks for theΔGbetween each adjacent state to

be plotted. The code defaults to the analysis of Gromacs files,

so that in thedhdl_filesfolder it expects to find files that start

with “dhdl” and have “.xvg” extension (e.g., dhdl_1.xvg,

dhdl_2.xvg,dhdl_3.xvg, etc.); this can however be changed

with the--pand--qflags. Moreover, free energy calculations

run with Amber [31], Sire (http://sire.org), or Desmond [81],

can still be analyzed by choosing the software with the--aflag.

The--fflag allows instead to plot the free energy estimate as a

function of time in both directions. These are just some of the

options available, and the reader can find an explanation for all

of them by displaying the help message of the script.

Acknowledgments

The EPSRC and Evotec via the Systems Approaches to Biomedical

Sciences Doctoral Training Centre (EP/G037280/1) support

M.A. J.B. is supported by the EPSRC/MRC via the Systems

Approaches to Biomedical Sciences Doctoral Training Centre

(EP/G037280/1) with additional support from GSK. We thank

David Mobley (University of California, Irvine), John Chodera

(MSKCC), and Michael Shirts (University of Colorado, Boulder)

for sharing their extensive experience on alchemical free energy

calculations through publicly available platforms and personal com-

munications. Work in PCB’s laboratory is currently supported by

Absolute Alchemical Free Energy 227