Web interfaces to molecular dynamics and quantum chemistry packages
Two popular programs for geometry optimisation and other fundamental structural properties are Gaussian and MOPAC. Extending the ideas developed elsewhere about chemical MIME types to specify input file types for Gaussian or MOPAC is straightforward. Thus by defining:-- chemical/x-mopac; xmol -readFormat mopii %s
- chemical/x-gaussian; xmol -readFormat gaussin %s
in a local .mailcap on a UNIX system (or its equivalent on other platforms) one can readily check the format of a gaussian or MOPAC job submission file. An example here is the input file for a restricted Hartree-Fock geometry optimisation run on Gaussian for the interesting molecule bisbenzenechromium. The file consists of a number of "option cards" (cards for christsake!) which describe the type of calculation to be run, and a title for the job, etc. The next block of data describes the initial geometry of the molecule (as a so-called Z matrix). Finally some initial guesses for the bond lengths and angles are given. We can check that this file correctly describes the molecule by invoking xmol. If you have edited your .mailcap and have xmol installed clicking here should spawn xmol as an external viewer (the file that is being read here is a symbolic link to the the gaussian input text file above but with a file extension ".gau").
Xmol can also convert between file formats so that one could read, for example, a ".xyz" file type and write a ".gau" file type. In the future this feature might be used to launch a remote job on a compute server. We can demonstrate how this might be done with a simple MOPAC calculation (an AM1 minimisation) on water. We have constructed a forms based interface, although other structures are no doubt possible, and you can test it here (It really works now ed.).
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