The Silicon Graphics Teaching Laboratory has been replaced by the Chemi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>'
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