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?
How to manipulate dihedral angles in pre-optimized molecule coordinates?
computational chemistry
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.