Keywords: viewmol

# 5 Synopsis

VIEWMOL can be called as follows:

      viewmol [[-bio | -dmol | -gamess | -gauss | -gulp | -mopac |
                -pdb | -pqs | -tm | -tmmsi | -vamp] file]

VIEWMOL has an automatic file format detection algorithm build in and should be able to identify output files of the programs supported without user intervention. VIEWMOL will also run Python scripts given on the command line when the Python script has the string `python` within the first 1024 characters (this is usually the case if the script starts with the common `#!/usr/local/bin/python` or similar first line). If VIEWMOL is called without parameters it will bring up a file selection box to select the file to be viewed.

If the option `-bio` is used the file name of a DISCOVER file has to be specified. One can use the `.car`, the `.cor`, or the `.arc` file of DISCOVER. VIEWMOL also looks for a file with the extension `.hessian` and tries to read the vibrational spectrum from it, if it was found.

If the option `-dmol` is used the file name of a DMOL/DSOLID/DMOL3 output file has to be specified.

If the option `-gamess` is used the file name of a GAMESS output file has to be specified.

If the option `-gauss` is used the file name of a GAUSSIAN 9X output file has to be specified.

If the option `-gulp` is used the file name of a GULP output file has to be specified.

If the option `-mopac` is used the file name of a MOPAC output file has to be specified. VIEWMOL also looks for a file with the extension `.gpt` and reads information about basis sets and MOs from it, if it was found.

If the option `-pdb` is used the file name of a PDB file has to be specified.

If the option `-pqs` is used the file name of a PQS output file has to be specified.

If the options `-tm` or `-tmmsi` are used the file name of a TURBOMOLE file containing at least the data group `$coord` has to be specified. `-tm` reads the original TURBOMOLE output while `-tmmsi` allows VIEWMOL to read TURBOMOLE outputs from the TURBOMOLE version distributed by Accelrys (the only difference is the ordering of the normal modes in the `control` file).

If the option `-vamp` is used the file name of a Vamp output file has to be specified. VIEWMOL also looks for a file with the extension `.gpt` and reads information about basis sets and MOs from it, if it was found.