ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov Copyright © 2020, Molsoft LLC Jun 5 2024
|
A chemical table or an .sdf file can be converted to 3D and sampled using the conformational generator with
the _confGen script provided with the ICM distribution.
Syntax:
icm _confGen input.sdf output.sdf [options]
Options:
- auto=(0) : number of rotatable bonds to auto switch between systematic and MC. 0:always MC
- effort=(1.) : the relative mc sampling effort. Increase to 3. or 10. for more rigorous sampling
- maxenergy=(10.) : skip conformations with higher than 10. kcal/mole energies from the base
- mnconf=(50) : the maximal number of conformers per compound
- sizelimit=(80) : do not sample bigger molecules than atoms
- vicinity=(30) : [deg] the torsion root-mean-square deviation threshold for cluster size.
- -c : improve geometries and energies with Cartesian MMFF minimization
- -d : sample cis/trans for Double bonds
- -e : only evaluate conformational Entropy for compound (no poses)
- -f : Force overwriting of the output file
- -h : Help
- -I : force update of the Input data file index
- -q : Quiet (suppress warnings)
- -r : sample flexible Ring systems
- -s : use Systematic search instead of MC
- -S : evaluate Strain of this particular conformation from 3D mol file (implies -keep3D)
- -v : verbose (show commands).
- -fr=.. -to=.. from and to indexes of the database to be screened.
- -hydrogen : keep hydrogens in the result table
- -keep3D : keep conformation from a 3D mol file
- -molcart=connect_string : host,user,pass,database
- -proc= : start n parallel threads
Example:
icm _confGen myligs.sdf myligconfs.sdf effort=5. -f
|