Equilibrium simulation of Protein Kinase A (PKA) in complex with protonated and deprotonated benzoic acid

Molecular Dynamics all atom simulation of Protein Kinase A (PKA) in complex with the ligands protonated benzoic acid, deprotonated benzoic acid (both PDB entry 5SNN)as well as benzamide (PDB entry 6SNX). The simulation was performed with Gromacs using the CHARMM36m Forcefield with ligand parameters generated by CGenFF. The water model is TIP3. The equilibration was performed in thee NVT and NPT ensemble for 100ps each. The production run was performed for 1 μs in steps of 2 fs.The integration was performed with the Leap Frog integrator. The temperature was kept at 300K with the Bussi-Donatio-Parinello velocity rescaling thermostat and the timeconstant of 2.0ps. The pressure was kept at 1bar using the fully isotropic Parinello-Rahman barostat with a timeconstant of 5ps and a compressibility of 4.6E-1 1/bar.