The relative hydration free energy of PHE and TRP was calculated using ligandswap. This is a program that comes with Sire that can calculate relative hydration and relative binding free energies of solutes / ligands.

All of the files used to perform the ligandswap calculation can be downloaded from here. You want do download the file “ligandswap.tar.bz2” and to unpack it into the current directory. This will result in a directory called “ligandswap” that contains all of the files for the calculation.

Ligandswap comes with Sire and can be run using the command;

Like quantomm, you can get help using the “--help” option. Ligandswap needs as input two topology/coordinate file pairs that contain the two ligands that will be swapped. The program constructs a λ coordinate that swaps one solute with another, thereby giving the relative free energy of the solutes. For our work, we calculated relative hydration free energies of PHE and TRP, so the PHE.top/PHE.crd and TRP.top/TRP.crd files were used as input, with the command contained in the file “run_ligandswap” used to perform the calculation. This command specified the names of the solutes to be swapped (PHE and TRP) and the topology and coordinate files that contained these solutes. The option “--vacuum” was used because ligandswap swapped the solute between being in the water box and being in vacuum (as we wanted a relative hydration free energy). If we were looking at relative binding free energies, then we would not use the “--vacuum” option, and the ligand would be swapped between being bound to the protein and being free in water (in this case, the topology/coordinate files used as input should be of the ligands bound to a protein).

The “output” directory contains the output of the ligandswap calculation. The calculation was performed in two stages; stage 1 swapped PHE in water with TRP in vacuum, while stage 2 swapped TRP in water with PHE in vacuum. The free energies for each stage were averaged and saved into the “output/stageX/freenrgs.s3” files and can be analysed using sire.app/bin/analyse_freenrgs.

The free energies for each stage were calculated simultaneously using thermodynamic integration (analytic fitted and quadrature-based), free energy perturbation (FEP) and using Bennett’s acceptance ratio (BAR) method. As the stage 2 free energy difference should be equal and opposite to the stage 1 difference (as it is the reverse process) this means that we have eight estimates of the relative free energy (four from each stage). The average of these eight estimates is -5.0 kcal mol-1, which is the MM value used in the rest of the workshop.

$SIRE/bin/ligandswap

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