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10.24 Ligand Energetics
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[ Conformational Entropy | Strain ]

Available in the following product(s): ICM-Chemist-Pro | ICM-VLS

10.24.1 Conformational Entropy


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.

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.

10.24.2 Strain


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.


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