Subject: Re: Babel

From: "John R. Nash" <[email-masked]>
Date: Thu, 1 May 1997 11:40:44 -0500

Jeff (and the rest of CCL) -

>The Babel program seems very easy to use.  For instance
>converting
>molgen files to pdb files.

Babel is indeed very easy to use, especially for freeware. Since it is
freeware, however, the quality of the individual modules is to some extent
based on how much testing was done by the authors and third parties.  For
example, the converters to and from Gaussian are very good, since lots of
people used them and gave feedback to the authors (who nicely went back to
the code and fixed things).  The CACAO converter is, unfortunately, much
less used, and it still has some problems.  I'm not sure what the current
status of Babel is; the authors have received their PhD's and are in the
industrial world now, and I haven't seen an update in some time.  You might
want to email the "babel" address at Arizona that's mentioned in the README
to see if anyone's answering.  I'll do some checking myself.  Since the
source code has always been available, it seems to me that development
could resume if someone else picked it up; maybe I'll have a look at the
code  after I graduate.

>However it stumbles converting molgen or
>mopac output files into C.A.C.A.O. files.  The commands
>babel -imolgen butane.mol -ocaccrt butane.in
>babel -imolgen butane.mol -ocaccrt butane.cor
>babel -imolgen butane.mol -ocaccrt butane.bin
>where each tried separately.  The last two files were inputted directly
>into the CACAO program without doing an extended Huckel(eh).
>The program issued the error message binary file corrupted, also the
>error message does not recognize atom type 6.

The extension you want for either internal or cartesian input to CACAO is
 .in.  The .cor and .bin are generated by the EH program when the EHMO
calculation is run.  Reading a file.in into CACAO without its .cor and .bin
will cause it to complain that it can't find the supporting files, but you
can still use it to view the structure to make sure that the geometry
transferred correctly. If you want to look at orbitals, you have to run the
EHMO program (EH . FILENAME); babel is only a geometry converter, and it
can't do anything with checkpoint files from qm programs.

I would suggest using the CACAO cartesian converter of Babel (as you are),
since the internal coordinates converter seems more broken.  What you will
get out is close to the input file you want, but there are still things
needed to be tweaked.  The input for CACAO 4.0 is Fortran format, so every
space counts (for example, carbon is "<space>C" not "C" since the element
field is two characters long).  Supposedly, a free-format CACAO is in the
works... any one seen an update?  My advice is to do what I do: use babel
to convert to CACAO cartesian, then go through the input file carefully,
using one of the CACAO example files that works as a guide.  The manual
tells explicitly what the program expects, so have that open when you do
it, too.  This is hardly ideal (I hate Fortran format!), but I have gotten
it to work for me.

One more note: if you want to look at Walsh diagrams, you have to use
internal coordinates (z-matrix).  As I said, the Babel CACAO internal
converter isn't quite working, so it won't be much help.  My suggestion is
to convert to Gaussian z-matrix and exit the file so it looks like a CACAO
one, keeping in mind that the way CACAO and Gaussian start and label their
zmat's is slightly different.

Good luck, and I hope this helps!

-john nash
almost a PhD, uw-madison chemistry

-==-John R. Nash-==[email-masked]==-UW-Madison Chem. Dept-==-
                 --- "When in doubt, roll!" ---