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university of cambridge  


   normal modes visualisation

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Normal Modes Visualisation

Cadpac and MOPAC will both perform normal modes analyses, which can be visualised using Eadfrith or other programs. First, however, files of the right format must be created, using the utilities cadpacNMA or mopacNMA as appropriate. These utilities were written by Mark Mackey.

Cadpac

CadpacNMA is a small program designed to make the analysis of molecular normal modes calculated using the CADPAC package easier. CadpacNMA outputs a MacroModel multistructure data file showing the normal mode of interest.

CadpacNMA takes as input a Macromodel data file and a CADPAC output file containing a normal mode analysis (either numerical or through second derivatives). Note that the Macromodel data file MUST contain the atomic coordinates as they were presented to CADPAC for the normal mode analysis, or the results will be nonsensical. It is suggested that the Macromodel file be generated directly from the CADPAC file using cad2mmod to avoid this problem.

The syntax is 'cadpacNMA <Macromodel file> <CADPAC file>'

MOPAC

MopacNMA is a small program designed to make the analysis of molecular normal modes calculated using the MOPAC package easier. MopacNMA outputs a MacroModel multistructure data file showing the normal mode of interest.

MopacNMA takes as input a Macromodel data file and a MOPAC output file containing a normal mode analysis (either numerical or through second derivatives). Note that the Macromodel data file MUST contain the atomic coordinates as they were presented to MOPAC for the normal mode analysis, or the results will be nonsensical. It is suggested that the Macromodel file be generated directly from the MOPAC file using 'mop2mm' to avoid this problem.

The syntax is 'mopacNMA <Macromodel file> <MOPAC file>'




© Goodman Group, 2005-2017; privacy; last updated December 7, 2017

department of chemistry University of Cambridge