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558. ECEPP/2: Empirical Conformational Energy Program
for Peptides (IBM 3090 Version)
by M. Jean Browman, Lucy M. Carruthers, Karen L.
Kashuba, Frank A. Momany, Marcia S. Pottle, Susan P.
Rosen and Shirley M. Rumsey. Write-up by Gerard F.
Endres. Resubmitted by Harold A. Scheraga, Cornell
University, Ithaca, New York 14853.
Converted by W. Hwung, Department of Chemistry, Indiana
University, Bloomington, Indiana 47405
This program is a direct conversion of QCPE 454 and has
been vectorized for use on the IBM 3090 with vector
facility. This system makes extensive use of IBM's
ESSL (Engineering and Scientific Subroutine Library).
The empirical potential energy functions, energy
parameters and geometry parameters used in this program
are described in the literature (F. A. Momany, R. F.
McGuire, A. W. Burgess and H. A. Scheraga, J. Phys.
Chem., 79, 2361 (1975) and G. Nemethy, M. S. Pottle and
H. A. Scheraga, J. Phys. Chem. (submitted). The
program treats linear polypeptides and those containing
one or more intramolecular disulfide linkages (cystine
residues) but not polypeptides with cyclic peptide
backbones. It reads as initial input a data set
containing standard coordinates and computation of
relative potential energy. The Standard Residue Data
supplied with the program consists of a basic data set
for 26 amino acid residues and 20 end groups and a
supplementary set of 10 amino acid residues. The data
set includes all of the amino acid residues commonly
found in the proteins and many end groups present in
synthetic polypeptides. If any residues or end groups
are not needed in a particular application, an
abbreviated set can be used. Any properly formatted
residue data can be substituted for the supplied data,
e.g., if the user does not wish to use the supplied
standard geometry.
The user supplies additional data specifying:
1. the number of conformations to be treated,
the desired amino acid sequence (including end
groups), and the designation of the
stereochemistry (D or L) of each amino acid
residue
2. the pairing of half-cystine residues in
intramolecular disulfide bonds
3. the initial conformation (by supplying values
of all dihedral angles)
4. which dihedral angles will be treated as
variable, i.e., will differ in subsequent
conformations
5. new values of these variables for each
subsequent conformation
The program calls a set of subroutines to generate the
atomic coordinates for each conformation using bond
lengths and bond angles defined in the standard data
set and the dihedral angles specified by the user.
Another set of subroutines is called to compute the
total conformational energy (ETOT) using empirical
potential energy functions. ETOT is computed as the
sum of the following component energies: electrostatic
(EES), nonbonded plus hydrogen bonded (ENB), general
torsional (ETOR), cystine bridge torsional (ECYSTR),
and a loop-closing potential for S-S bonds (ELOOP).
The repulsive part of the nonbonded interaction energy
is reduced by a factor of 0.5 if a particular
interaction is "1-4", i.e., between a pair of atoms
separated by only one bond whose rotation affects their
interatomic distance. A group of subroutines is used
to specify which interactions are 1-4 type for a given
polypeptide sequence.
The output of the program includes the atomic
coordinates, the total conformational energy, and its
five components for each conformation. The sample main
program can be modified to carry out grid searches,
compute conformational energy maps (f - y plots), or
(in combination with a function-minimizing subroutine)
find conformations corresponding to local energy
minima.
FORTRAN (IBM VS2.2 PUT8801)
Lines of Code: 4326
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