[ Conformational Entropy | Strain ]

Entropy of the conformational ensemble is calculated according to the regular thermodynamic formula i.e. kT log(Sum(Exp(-Ei/kT))), Ei is the energy of the i-th conformation over the ground state, summation is over all conformations. The method uses MolSoft's conformation generator _confGen.

To calculate the conformational entropy of chemicals in an SDF file or a chemical spreadsheet:

• Chemistry/Ligand Energetics/Conformational Entropy
• Choose either the Local Tables (loaded chemical spreadsheet) or {Files} (SDF file) tab.
• Enter the maximum number of conformations you wish to generate.
• Enter a vicinity value. For more information on vicinity please see the command language manual http://www.molsoft.com/man/reals.html#vicinity
• Enter a effort value. This relates to the length of sampling time.
• Check boxes for Sampling Rings or Systematic Search (instead of Monte Carlo).
• Click OK.

The calculation will then run and you will see a progress bar in the bottom right hand corner of the GUI or you can check the progress of the job go to Windows/Background. When the job has finished:

• A table will be displayed called entropies with a column called Conf Entropy. The energy is in kcal/mol.
• The number of generated conformations (NofConf) is reported along with the spectrum of their force field energies (Energies)

There is no particular cutoff for entropy, the entropy numbers should be viewed comparatively - in a pair of compounds lower entropy is, of course, better.

Strain samples conformations of (each) ligand and uses lowest found energy conformer as a reference (energies are minimized and calculated per MMFF94s).

To calculate the conformational strain of chemicals in an SDF file or a chemical spreadsheet:

• Chemistry/Ligand Energetics/Strain
• Choose either the Local Tables (loaded chemical spreadsheet) or Files (SDF file) tab.
• Enter a effort value. This relates to the length of sampling time.
• Check the Systematic Search option if you do not want to use Monte Carlo search.

The calculation will then run and you will see a progress bar in the bottom right hand corner of the GUI or you can check the progress of the job go to Windows/Background. When the job has finished:

• A table will be displayed called strain with a column called Strain. The energy is in kcal/mol.