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I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure with optimal geometry of random small chemicals (say 30 atoms)? I found http://cccbdb.nist.gov/mdlmol1.asp but it selects mol files from a limited database. I need a command line UNIX program which computes mols from formulas.

Concise structural formulas popular during past ages are unable to describe every type of chemical structure like morphine. I found no software that supports csf (Smiles and inchi are popular but are encoded and not human readable). When the bonds of the structure are known geometric minimization (DG-AMMOS) orients the structure to a stable native like direction. http://www.mti.univ-paris-diderot.fr/fr/downloads.html

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    $\begingroup$ Am I reading this right, you have chemical formulas and want to get a set of 3D coordinates (of the energy-minimized conformation)? $\endgroup$
    – Mad Scientist
    Commented Mar 11, 2013 at 10:12
  • $\begingroup$ @MadScientist yes that's correct but its not possible for all molecules just some $\endgroup$
    – user1357
    Commented Mar 12, 2013 at 5:03

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Did you try to use Bioclipse:

Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. Bioclipse supports editing in 2D, processing large collections of molecules in tables, calculation of various types of properties, and much more cheminformatics functionality. The Jmol application is integrated in Bioclipse as an editor, and provides advanced interactive 3D visualizations.

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For the reference, there is also USPEX, which works for a wide variety of molecular and continuous structures (mostly inorganic, though).

USPEX can be used to predict stable crystal structures at given P-T conditions, knowing only the chemical composition (or to predict both the stable compositions and structures, given the element types). USPEX can also be used for finding low-energy metastable phases, as well as stable structures of nanoparticles, surface reconstructions, molecular packings in organic crystals, and for searching for materials with desired physical (mechanical, electronic) properties.

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