Absolute and relative entropies from computer simulation with applications to ligand binding.
A comparison between two related methods, Schlitter's formula and quasiharmonic analysis, for calculating absolute entropies from the covariance matrix of atomic fluctuations using molecular dynamics (MD) simulations is presented. Calculations for a set of organic compounds in the gas phase are compared to the corresponding statistical thermodynamics results for translational and rotational entropies and to experimental data for vibrational entropies. Encouraging agreement is obtained for translational entropies, but for the rotational contribution, both methods fail to reproduce the theoretically calculated values. Absolute and relative vibrational entropies are found to be better reproduced using quasiharmonic analysis compared to Schlitter's formula. For rotational entropies, we propose a method based on the variances in Euler angles, which gives good agreement with theory. Alternative methods for estimating translational entropies based on principal root mean-square (rms) fluctuations of the center of mass are also presented, and these reproduce theoretically calculated values well. These methodologies are applied to the binding of benzene to T4-lysozyme, where close agreement with the literature is obtained for translational and rotational entropies.
Carlsson
Jens
J
Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
Aqvist
Johan
J
D017122:Bacteriophage T4 / Q000201:enzymology / Q000235:genetics; D001554:Benzene / Q000737:chemistry / Q000378:metabolism; D003198:Computer Simulation; D008024:Ligands; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D013816:Thermodynamics
D008024:Ligands; D009113:Muramidase; D001554:Benzene