Three-dimensional molecular structures can be built in the computer with molecular editors. Molecular editors are sophisticated programs that understand chemical concepts such as connectivity, valence, and atom types. Many commercial programs come with built-in molecular editors. For example, SYBYL from Tripos has its own molecular editor.
Few molecular editors are freely available for academic use. One such popular program is MOLDEN by Gijs Schaftenaar. Another program that is convenient when building or editing biological molecules, such as peptides is PyMOL. Both programs provide capability to build molecular structures from scratch and save the structures in many different formats. In this tutorial we will learn how to build small molecules with MOLDEN.
MOLDEN by Gijs Schaftenaar |
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Molden Graphical Window |
MOLDEN Z-Matrix editor |
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MOLDEN gives the user the ultimate control over building the molecular structure: every distance, angle and dihedral can be specified in the Z-matrix editor. Molecular mechanics or quantum mechanics calculations can be launched directly from the builder. |