OPEP Files Generator


This automatic tool will allow you to generate the OPEP files of your system required to use the ART, MD or REMD softwares
based on the OPEP potential. Four files will be created for a system 'pepxx' : pepxx.top, pepxx.list, pepxx.pdb, ichain.dat,
all of which will be tared and compressed in a file pepxx.tgz. A link to this last file will be sent to your email address

A beta version of the generator for peptides containing disulfide bonds is now available here

Use OPEP potential v3 : Compatible up to simulateur v1.95
v4 : Compatible with simulateur v2.0+
From a properly
formated .pdb file :
Use position from .pdb
file as template
In the .pdb file, peptides must be separated
by a
"TER" line. If more then one MODEL
is present, the first one will be used.
From a .txt file
containing the sequence :
In the .txt file, peptides use the 3-letters
amino acid representation and can span
multiple lines.
Each peptide must be separated by
a
"TER" line in the .txt . Non zwitterion
peptides must start with the
"ACE" code
(for -COCH3) and end with either
"NHE" (-NH2) or "NME" (-NHCH3)
Input file path(.pdb/.txt):
Manually entering
the sequence :
Use the same rules as the .txt file. Example:

ALA ALA ALA ALA ALA
TER
ACE ALA ALA ALA
ALA ALA NHE
TER
VAL GLY ALA GLY GLY VAL

Padding between peptides : Minimum spacing between peptides,
between
1.0 and 100.0 angstroms
use
0.0 to disable (not recommanded)
Valid email address : im@validaddress.com
Title / Descriptor Optional, will be in the email's subject line
SIMULATEUR v1.6+ ONLY! Last update Jan 16th

This automatic procedure was designed by Jean-Francois St-Pierre1, Normand Mousseau1, and Philippe Derreumaux2.

Details of the force field can be found in:
  • P. Derreumaux, J. Chem. Phys. 111 : 2301-2310 (1999)
  • S. Santini, G. Wei, N. Mousseau, P. Derreumaux, Internet Electron. J. Mol. Des. 2 : 564-577 (2003).
  • J. Maupetit, P. Tuffery, P. Derreumaux, Proteins: Structure, Function and Bioinformatics 69(2) : 394-408 (2007)
  • OPEP version 4: Y. Chebaro, S. Pasquali, P. Derreumaux, to be published
1Departement de Physique, Universite de Montreal, C.P. 6128, Succursale Centre-Ville, Montreal, Quebec H3C 3J7, Canada
2Laboratoire de Biochimie Theorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique,
Universite de Paris 7 Denis Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France