ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov Copyright © 2020, Molsoft LLC Nov 14 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.
- -b : same as -c (see below) but without bond lengths (only angles and torsions)
- -c : improve geometries and energies with Cartesian MMFF minimization
- -d : sample cis/trans for Double bonds (not needed 'as drawn' is OK)
- -e : only evaluate conformational Entropy for compound (no poses)
- -f : Force-overwrite of the output file
- -h : Help
- -q : Quiet (suppress warnings)
- -p : optimize pyramidal molecular geometry (set automatically by -S or -e options)
- -r : sample flexible Ring systems
- -s : use Systematic search instead of MC
- -v : verbose
- -A : use AI-assisted sampling instead of torsion stochastic sampling
- -C : set formal charges according to pKa model. Use if you do not trust the charge defined by the chemical structure as drawn.
- -H : sample polar hydrogens
- -I : force update of the Input data file index
- -S : evaluate Strain of this particular conformation from 3D mol file (implies -keep3D)
- -V : shows script 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:
icm64 _confGen input.sdf output.sdf effort=5. -A -H -r -C -c -f
|