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 wrong.
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 E-mail: sampieri.f@jean-roche.univ-mrs.fr Fax: (33) 4 91 65 75 95 Tel: (33) 4 91 69 88 44