4.2. Molecular Dynamics and Free Energy Calculations

Poses from the docking studies were prepared for the forcefield OPLS/AA [18] from the program GROMACS [19,20] (Version 5.1.4, Stockholm University and KTH, Stockholm, Sweden; Biomedical Centre, Uppsala, Sweden; Science for Life Laboratory and KTH, Stockholm, Sweden, 2016), following the same procedure as before [12], using ACPYPE [21,22] and MKTOP [23]. The complexes HssAChE/ligand were simulated through GROMACS 5.1.4 [19,20] according to the same protocol used before [12,24], and results were analyzed with the software VMD [25] (Version 1.9.3, NIH resource for Macromolecular Modeling and Bioinformatics, University of Illinois, Urbana-Champaign, IL, USA, 2016), Grace (http://plasma-gate.weizmann.ac.il/Grace/) (Version 5.1.25, Grace Development team, Weizmann Institute of Science, Baden, Austria, 1995–2015) and PyMOL [26] (Version 1.7.x, Schrödinger LCC, New York, NY, USA, 2009–2014).

As before [12], the MM-PBSA [27] calculations were accessed through the s_mmpbsa tool [27] from the GROMACS package [19,20].