Empirical force field parameters
for the proteins were CHARMM36,50 (link) ligand
molecules were derived from CGenFF,51 (link) and
water was treated using the TIP3P model.52 Protein preparation simulations were performed using CHARMM53 (link) (section S1, Table S1 ), while the production phase of the GCMC/MD simulations were performed
using in-house code for the GCMC and GROMACS54 for the MD portions of the calculations. The protein systems are
immersed in an aqueous solution (along with the lipid membrane and
cholesterol in case of the GPCRs) containing approximately 0.25 M
of each of the small solutes: benzene, propane, acetaldehyde, methanol,
formamide, imidazole, acetate, and methylammonium.
for the proteins were CHARMM36,50 (link) ligand
molecules were derived from CGenFF,51 (link) and
water was treated using the TIP3P model.52 Protein preparation simulations were performed using CHARMM53 (link) (
using in-house code for the GCMC and GROMACS54 for the MD portions of the calculations. The protein systems are
immersed in an aqueous solution (along with the lipid membrane and
cholesterol in case of the GPCRs) containing approximately 0.25 M
of each of the small solutes: benzene, propane, acetaldehyde, methanol,
formamide, imidazole, acetate, and methylammonium.
