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I want to explore the low energy states of an amino acid or a peptide by generating input geometries, defined by multiple dihedral angles of the backbone or the side chain. From these starting conformations I want to do geometry optimization to yield local energy minimum geometries.
The following approaches failed:

  • Using the ModRedundant keyword in the Gaussian09 package to define new values for the dihedral angles. This crashes for larger molecules and major changes in the coordinates.
  • Detecting the substructure of the molecule (e.g. the backbone) by SMILE / SMARTS pattern and using obrotate from the openbabel package to change the values. Works fine for a single dihedral or maybe two, but afterwards these changes the pattern of the substructure is not necessarily detected anymore and no further dihedral angle can be changed.
  • Usage of a well chosen Z-Matrix: The great disadvantage is, that I don't know how to yield a Z-Matrix with the wanted dihedrals from a given geometry and therefore I can't start from a pre-optimized structure.

Are there any other attempts to this problem?

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1 Answer 1

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I did this stuff by a self-made script for a long time (but had to prepare the input manually for every molecule).

Meanwhile, I came along confab.

Confab is an open source conformation generator whose goal is the systematic coverage of conformational space.

A detailed description how it works can be found in the authors publication.

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  • $\begingroup$ This is not really an answer to the question. Why don't you explain in a bit more detail the approach you ended up using (maybe even with code or pseudocode)? That way, your answer would be of help to other users with a similar problem (this is, after all, what StackExchange is for), and maybe someone even has an idea how to avoid some of that manual work. $\endgroup$
    – Christian Clason
    Jun 20, 2013 at 12:34
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    $\begingroup$ In case you are not familiar with the StackExchange network: The downvote is a sign that the answer in its current form is not seen as helpful - it can (and will) be removed if the answer is edited appropriately. Self answers are perfectly fine (and even encouraged and likely to be upvoted), as long as they are a useful contribution to the site. $\endgroup$
    – Christian Clason
    Jun 20, 2013 at 12:40

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