Subject: RE: Potential energy calculations with MODELLER
From: "Andrej Sali" <>
Date: Wed, 16 Jan 2002 15:10:06 -0500
Cc: "Andrej Sali" <>, "Bozidar Jerkovic" <>
Organization: Rockefeller University
A MODELLER TOP script can relatively easily iterate over reading a pdb
file, doing an energy calculation, and printing out the results, for
many input pdb files. But the problem is getting the "true" CHARMM
energy out of MODELLER.
1) The CHARMM terms in the MODELLER objective function are only a subset
of all the CHARMM terms (there are only bond length, bond angle, and
impropers in the default MODELLER objective function constructed for
homology modeling, though one could add the dihedral angle,
Lennard-Jones, and Coulomb terms by selecting the right options; I think
CHARMM also uses some fancy cross-term bond angle terms which are not
implemented in MODELLER).
2) The CHARMM terms are strictly speaking meant for the all-atoms
models (including hydrogens), so I think one should build hydrogens
before assessing MODELLER models with CHARMM.
3) MODELLER does not have the latest CHARMM force field.
4) You probably need to minimize a MODELLER model in CHARMM, just a
little bit, before evaluating its energy (otherwise it would
So, I think it would be best if you do the energy calculations in
CHARMM. Also, there is a web server (EEF1 server or so ...) here in NYC
by Themis Lazaridis, which may give you want you want (maybe not for
thousands of structures?)?
Hope things are going very well for you!
Best wishes, Andrej
Andrej Sali, Associate Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail ; http://salilab.org
[">mailto:] On Behalf Of
Sent: Wednesday, January 16, 2002 1:08 PM
Subject: 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!
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