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[Licence| Download | New Version Template] aceo_v1_0.gz(27 Kbytes)
Manuscript Title: Molecular associations.
Authors: S. Fraga
Program title: AMYR
Catalogue identifier: ACEO_v1_0
Distribution format: gz
Journal reference: Comput. Phys. Commun. 29(1983)351
Programming language: Fortran.
Computer: AMDAHL 580/5860.
Operating system: MTS.
RAM: 104K words
Word size: 32
Peripherals: disc.
Keywords: Molecular interactions, 1/r expansion, Steepest-descent Energy minimization, Structure, Biology.
Classification: 3, 16.1.

Other versions:
Cat Id Title Reference
ACBG_v1_0 AMYRVF CPC 66(1991)341

Revision history:
Type Tit le Reference
adaptation 0001 AGAB See below

Nature of problem:
Determination of the stable conformations of the association of two molecules.

Solution method:
The stable conformation(s) of the molecular association is (are) found by minimization of the energy of interaction between the two molecules. The energy is evaluated by means of a 1/R expansion (with R**-1, R**-4, R**-6 and R**-12 terms), with coefficients obtained by fitting of accurate SCF results. The energy minimization is carried out by a steepest-descent method.

Restrictions:
Calculations should be restricted to molecules consisting of atoms belonging to the thirty classes for which expansion coefficients are available.

Unusual features:
This program has been prepared from a version, in operation at the University of Alberta, which runs on a FPS-190L array processor and produces the plots of the conformation of the molecular complex on a Tektronix T-4015-1 terminal adapted with a hard copier. The orginal program may be easily regenerated from this published version.

Running time:
310 s for the test run (with three cases).

ADAPTATION SUMMARY
Manuscript Title: Association of proteins: adaptation and coupling of two available programs.
Authors: L. Seijo, B. Coghlan, S. Fraga
Program title: 0001 AGAB
Catalogue identifier: ACEO_v1_0
Distribution format: gz
Journal reference: Comput. Phys. Commun. 41(1986)169
Programming language: Fortran.
Computer: AMDHAL 580/5860.
Operating system: MTS.
Word size: 32
Classification: 3, 16.1.

Nature of problem:
Determination of the optimal spatial conformations and relative positions of two proteins from their amino acid sequence.

Solution method:
In a cycle, the internal structure of each protein is optimized in the presence of the other protein, then their relative position is changed. Optimization of a single protein is performed, under an energy criterion, by rotation around the bonds C alpha-C', C'-N, N-C alpha and C alpha-C Beta (Comp. Phys. Commun. 36(1985)391). Translation and rotation of one protein with respect to the other is governed by the gradient of the interaction energy between them (Comp. Phys. Commun. 29(1983)351).

Restrictions:
The ones in the original programs.

Unusual features:
It can also be used to optimize the structure of a single protein in the presence of an other molecule which is not a protein.

Running time:
Dependent on the size of the proteins. CPU times for the three test cases are 49, 275 and 201 s.