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Potential energy calculations with MODELLER

Hi and Greetings to all !

I used MODELLER to generate a huge number (3500 pdb files) of models of
the same protein with 7 different disulfide pairings (500 models of each
pairing), and now I have to sort the models according their potential
energies (bonded + non-bonded) in vacuum.
I initially thought of using a molecular mechanics software in standalone
mode to be lauched on each pdb file by a perl script, and then collect the
energy values in whatever format the software created.
I start looking for such a program which should be:
- executable for SGI 02 R10K (IRIX 6.5);
- free for academics;
- launchable from a Perl script;
But I didn't found such a jewel (oh no!, not such of highest value as
MODELLER!) on the Web.
So I come back to MODELLER, though its top script mode didn't seem the
simplest way to me to achieve batch energy calculations, but I hope I'm

Could anybody suggest a method to use MODELLER for computing (CHARMM)
potential energy of billions of structures in pdb format?

Many thanks in advance!

François Sampieri

UMR 6560 CNRS-Universite de la  Mediterranee
Laboratoire de Biochimie - IFR Jean Roche
Faculte de Medecine Nord
Bd Pierre Dramard
13916 Marseille Cedex 20
Fax: (33) 4 91 65 75 95
Tel: (33) 4 91 69 88 44