Additional helper applications may be used in the Z-matrix Editor to optimise the stuctures on a force field level. It is also possible to start up Ab Initio/Semi Empirical packages from the Z-matrix Editor. Molden should know where these programs are in order to use them. This is done by setting UNIX environment variables (So this doesnt work for the Windows-NT/95 and OS2 versions). The best way to do this is to rename the molden executable to molden.exe and call this from the molden wrapper script:
#!/bin/csh # setenv TNK_ROOT /compchem/1/tinker setenv TA_ROOT /compchem/1/sybyl63 #setenv QNT_ROOT /mnt/compchem1/msi/quanta96 #setenv g94root /cmsc #setenv g98root /cmsc setenv g03root /cmsc setenv MOPAC_ROOT /compchem/1/mopac93 setenv GAMESS_ROOT /compchem/1/gamess # /usr/local/bin/molden.exe $argv #
PS: Be sure there is no "stty" line in your .cshrc file, if there is move it to your .login file where it belongs
Molden will look for executables in the directory $TNK_ROOT/bin and parameters
in $TNK_ROOT/params. Molden uses the MM3 implementation in tinker (MM3-1992)
. There are often parameters missing for MM3 in tinker (when dealing with a protein it will write out tinker_charmm file).
Molden will create the files molin.xyz (the tinker input file) and
(A C-shell script that executes the tinker program). There is still time to change or add to these files when molden pops up a window with the text "Setup complete, click OK to optimise". After executing tinker the following files will be created:
molin.xyz_2 the tinker file with the optimised structure, molden will automatically map this to the current z-matrix,
tinker.log this file will tell you if anything went wrong (insufficient parameters etc). At present molden doesnt warn you when things go wrong.
Some tinker MD xyz files can pose a problem to moldens automatic cartesian to Z-matrix converter and cause molden to hang. Use the -a commandline flag to turn off the automatic cartesian to Z-matrix conversion.
Molden will look for a script $MOPAC_ROOT/bin/mopac.csh.
Molden will create the files jobname.dat (the mopac input file)
(A C-shell script that executes the Mopac program). There is still time to change or add to these files when molden pops up a window with the text "Setup complete, click OK to optimise". After executing mopac the usual files will have been created. Molden will not automatically read in the outputfile on completion of the job.
Molden will look for a script $GAMESS_ROOT/utilities/rungamess.
This will NOT work for GAMESS-US.
Molden will create the files jobname.in (the gamess-uk
input file) and jobname.run
(A C-shell script that executes the Gamess program). Molden will not automatically read in the outputfile on completion of the job.
Molden will look for either of the files:
$g09root/g09/bsd/g09.login $g03root/g03/bsd/g03.login $g98root/g98/bsd/g98.login $g94root/g94/bsd/g94.login $g92root/g92/bsd/g92.loginMolden will create the files jobname.com (the gaussian input file) and jobname.run