- #STOPPING CHEMDOODLE FROM AUTO ADDING HYDROGENS UPDATE#
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The FIRE optimizer differs from the other optimization methods described here in that it does not employ a line search. A new optimizer for the molecular modeling engine is implemented, FIRE (Fast Inertial Relaxation Engine).New bond order perception algorithms are now available, including "All Single", Antechamber and Auto-UFF. menu item or opening a file with no bond information.
Bond deduction has been significantly improved, allowing options for enforcing maximum valencies and changing the bond distance tolerance when using the Molecule>Deduce Covalent Bonds. menu item, choose the mapping algorithm, whether to overlap the structures, or allow inversions. A new function to align molecular structures in 3D. While minimizations of several discrete structures using through-space forces may look correct, please understand the theory behind the force field you are using and that any force field not specifically developed or parameterized for intermolecular forces will not lead to experimentally accurate coordinates. Please note, while you are able to optimize the entire scene, most force fields are not parameterized for multiple discrete molecular structures, and you will be relying on the through-space forces defined in the force field (mainly van der Waals and electrostatic), if defined at all. 
To do this, you can change the optimization scope to optimize the entire scene. However, you may wish to optimize several discrete molecular structures at the same time and in relation to each other. ChemDoodle 3D therefore will optimize molecular structures separately and individually as you are editing them. Most small molecule force fields are optimized for describing individual discrete molecular structures.
#STOPPING CHEMDOODLE FROM AUTO ADDING HYDROGENS FULL#
ChemDoodle 3D now allows full scene modeling simulations. Major new features include the ability to perform full scene modeling simulations, an implementation of the FIRE optimizer, 3D molecular structure alignment, improved bond deduction with new bond order perception algorithms, and more. #STOPPING CHEMDOODLE FROM AUTO ADDING HYDROGENS UPDATE#
ChemDoodle 3D v6.6 is a feature update to ChemDoodle 3D.
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