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Article ID: 821 - Last Modified: May 17, 2011

Can I calculate the translational, rotational, and vibrational energies of molecules?

Yes. MacroModel (molecular mechanics) includes the RRHO feature, which calculates the translational, rotational, and vibrational enthalpy, heat capacity, entropy, partition function, -TdS, and free enegy using a rigid rotor, harmonic oscillator approximation. The calculation takes a single structure as input. The vibrational calculation ignores the first six frequencies. The output energy values are written in the jobname.log file, and added as properties to the output structure file. Additional information is printed to the jobname.mmo file if RRHO arg1 is set to 1.

There is a related python script, RRHO_entropy.py, located on the Script Center, which calculates the change in translational, rotational, vibrational, and total entropy of ligands upon binding. The input is a pose viewer file (Glide output). The output energies are listed in the jobname.csv file, and included in the output structure file.

Jaguar (quantum mechanics) and QSite (QM/MM) also generate thermodynamic quantities when you do a frequency calculation. These values are included in the output text file and are added as properties to the output structure file.

Keywords: energies, MacroModel, Glide, entropy, enthalpy

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