Sep 13 2018
To generate a series of conformers for a ligand(s):
- Select the compounds (row(s)) you wish to generate conformers for in an ICM Molecular Table . Or to convert a whole table of compounds select Chemisty/Generate 3D Conformers menu.
- Right click on the selected row(s) and Chemistry/Conformation Generator (selected rows) and a data entry window as shown below will be displayed.
- 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 . Density of conformers is controlled by vicinity= parameter. Currently it always operates in terms of torsion RMSD, default is 30 degrees angular RMSD. Note that we only generate local minima, therefore reducing vicinity below some level will typically not produce any new conformers.
- Enter a effort value ( thoroughness in releases before 3.8-2) . This relates to the length of sampling time. Effort multiplies the sampling length determined by default heuristic based on size and number of torsions.
- Check boxes for Sampling Rings, Systematic Search, Cartesian Refinement (http://www.molsoft.com/man/reals.html#vicinity),Sample Cis and Trans, sample Pyramidal and Verbose (Display Warnings). The 'Cartesian' flag enables cartesian minimization/refinement of conformations (produced by torsion-only sampling). This should be checked whenever energetics is of importance. Torsion-only sampling is fast but only gives qualitative sample of accesible conformational space, relative energies of different conformers may not be accurate.
- Click OK and the sampling will be undertaken in the background - see Windows/Background Jobs
- Once the sampling has finished a table as shown below will be displayed. Click in the toggle boxes in the column labeled "L".
To display more than one 3D structure at a time use the row selection options.