ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Jan 4 2018

Contents
 
Introduction
Reference Guide
Command Line User's Guide
 ICM-shell
 ICM graphics
 Str.Analysis
 Sequence
 Molcart
 Pharmacophores
 Energy
 Molecules
 Animation
 Symmetry
 X-ray
 Plotting
 Docking/VLS
 Examples
 _chemSuper
 Chemical Conformation Generator
References
Glossary
 
Index
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Chemical Conformational Generator
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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:

_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


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