Expert's
Corner
Index | Conformation | Position | Divers | Descriptors | Substituents | Regression | Mine | Xray | Peptides | Docking | Fragments | Template | Ab ovo Moloc
Home
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 For a basic, though somewhat outdated, general description see Tutorial for the conformation module.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.
The batch program Mcnf serves to generate conformations automatically for a set of structures. It is described at the end of this page.

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).

Automatic Conformation Generation with 'Mcnf'

The program Mcnf reads a file containing structures and produces for each of them a set of conformations which are written into a result file of the same format. .sd- (default), .mab-, and .mol2-formats can be handled. The program can be used in redirection mode (taking input from 'stdin' and writing the results onto 'stdout') as a module in a pipe of programs.
It works exclusively in the stochastic mode, i.e. by randomizing atomic coordinates followed by energy minimization. When using .sd format, a datafield (MCNF) is added to each conformation containing its energy value. As with all of Moloc's batch programs, usage instructions are obtained by running the program without arguments.