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454. ECEPP: Empirical Conformational Energy Program
for Peptides
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. 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 residue information to be used in the subsequent generation of atomic 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 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 IV (ANSI) Lines of Code: 4500 |