We are pleased to introduce version 6.1 of our ChemDoodle 3D software. This update is free for all ChemDoodle subscriptions, Lifetime and Site licenses. Licenses are as little as $18, and we have a free trial available at: https://www.chemdoodle.com/3d


Executive Summary

ChemDoodle 3D v6.1 is a significant update to ChemDoodle 3D with a focus on the molecular modeling engine. Notable additions include parallel processing support, an implementation of the General Amber Force Field, improved Minimizer widget performance, and a new tool for easily twisting bonds to change torsion angles. This update is recommended for all users.


  1. Support for parallel processing of our force field calculations leading to significant runtime reductions. This parallelization is for the faster optimization of a single system. For instance, if your large molecule was optimized in x seconds, you may now use ChemDoodle 3D with parallel processing to optimize the same molecule in a fraction of x seconds. Parallel processing is very powerful, but needs to be understood to be used correctly. Please read section 5.6.3 of the ChemDoodle 3D User Guide for a full explanation and analysis.
  2. An implementation of the General Amber Force Field (GAFF) is now available in ChemDoodle 3D. This implementation is accurate, except we use Gasteiger-Marsili charges instead of the recommended RESP or AM1-BCC charge models. We hope to include AM1-BCC charges in the future. The theory of the GAFF force field is not perfect, as the authors demonstrate several issues with atom typing, and the parameter set (we use the antechamber v1.8 parameters in ChemDoodle 3D) is not complete, so molecules that are fully typed may still not be compatible as an inversion or torsion may not be handled. The GAFF force field is mainly used with the Amber force field for proteins and nucleic acids, and Amber comes with its own tools for GAFF functions, so the GAFF implementation in ChemDoodle 3D is mostly an academic exercise for us. Please see section 5.3.2 of the ChemDoodle 3D User Guide for more information.
  3. A new easy-to-use tool for twisting bonds and controlling torsion angles. Mix this with the Minimizer widget to observe rotational energy profiles and calculate barriers to rotation. Section 9.6.4 of the ChemDoodle 3D User Guide.
  4. New content function for linearly compacting all objects in the scene. Linearly compacting all content in the scene will place all content in a line with minimal spacing between each item. Section 9.4.1 of the ChemDoodle 3D User Guide.
  5. New content function for gridding all objects in the scene. Content will be partitioned into a grid with row and column counts you define, from left to right, then top to bottom. If there is more content than the total spaces available in the defined grid, the remainder will stack in the z direction, away from the camera. Each "cell" in the grid will have the amount of space equal to the largest item in the grid. A small buffer space pads each "cell". Section 9.4.2 of the ChemDoodle 3D User Guide.
  6. Edit atom coordinates by form to exactly define values. You can do this for all atoms in the scene, a selection of atoms, or individual atoms. Section 9.6.5 of the ChemDoodle 3D User Guide.
  7. The dielectric constant for electrostatic calculations in force fields can now be defined in the Preferences window under the Functions tab.


  1. The Minimizer widget and auto-optimize system has been refined to be quicker, more efficient and more responsive. Corrected the issue where changing force fields didn't update atom typing until the following repaint, if enabled. Changing force field parameters will now see immediate updates to the graphics. Previously, scenes with large molecules would interact slowly when the Minimizer widget was visible, and the auto-optimizer was off. This has been significantly improved.
  2. The molecular modeling chapter (chapter 5) of the ChemDoodle 3D User Guide has been rewritten to be more informative and thorough.
  3. Multi-structure content from MolGrabber and other sources will now be linearly compacted when placed into the scene and 3D coordinates are generated. This stops the structures from being too far away from each other.
  4. Corrected issue with printing images from ChemDoodle 3D on high-DPI screens.
  5. Fixed print preview issue where a doubling of the image appeared. This error only affected the preview.
  6. Corrected issue where the workspace could corrupt if an external monitor where ChemDoodle 3D was being displayed was disconnected.