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Conformation

Conformation Analysis

General remarks

The menu cnf contains various options to generate and analyze conformations of structures in a rather general sense. For a basic, though somewhat outdated, general description see Tutorial for the conformation module. In this exercise we show how to generate conformations of a molecule and an example how to analyze those. A file of the Molecule Trimethoprim (trimethoprim.mab) can be found in the moloc/dat directory.

Setup of a Conformation Run

The method of stochastic conformation generation is straightforward and for a description of the ring/loop method see the first reference on conformational analysis.

Analyze Conformations

It should be mentioned, that the same type of analysis can be performed in menu 'mch/l' in case the conformations are given as separate entries which may originate from an external program or from expanding a conformation library via 'cnf/m/e'. The result is then an entry-set, the entries of which can be stored e.g. in a multi-entry file (several possible formats).