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29.1.1 cmploop – Preliminary Analysis of CGEN Files

The cmploop command provides a simple method to analyze CONGEN conformation file. The syntax is

     cmploop [/b] [input-file [output-file]]

If no input-file is specified, the program defaults to congen.crd, and if no output-file is specified, then standard output on Unix machines or SYS$OUTPUT on VMS machines is used.

The program will read the CONGEN conformation file specified as the input-file and it will compute the RMS difference between each conformation in the file and reference coordinate set stored in the beginning, see Conformation File, for more information. The RMS difference is computed only over those atoms which are defined in both coordinates and which are different. If there are no such atoms, as might be the case when the reference coordinate set is empty, then the RMS is reported at 9.999. The /b switch directs the program to use just backbone atoms; N, C, and CA.

cmploop also reports the energy of each conformation as evaluated by the last EVL degree of freedom used in the search, see Evl Degree of Freedom. It will also display the torsion angles for all backbone degrees of freedom used.

Frequently, one is interested in the conformations with the lowest energy or RMS deviations. See Sortn, for a command that will sort the output of cmploop by these values.

Since cmploop computes RMS deviations over only those atoms which have different coordinates, it can report different RMS deviations than a COOR RMS command using the same atoms, see Coordinate Manipulations.