Normal mode analysis of alkenes by the consistent force field

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of Cα atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.

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Genetic refinement of the molecular force field: Normal mode analysis of purine vibrations

Biospectroscopy ◽

10.1002/(sici)1520-6343(1997)3:1<61::aid-bspy5>3.0.co;2-v ◽

1997 ◽

Vol 3 (1) ◽

pp. 61-71 ◽

Cited By ~ 2

Author(s):

B. Brutovský ◽

J. Uličný ◽

P. Miškovský ◽

V. Lisý ◽

L. Chinsky

Keyword(s):

Force Field ◽

Normal Mode ◽

Normal Mode Analysis ◽

Mode Analysis ◽

Molecular Force ◽

Molecular Force Field

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Vibrational Dynamics of 2-[3-(p-flourobenzoyl) Propyl]-1,2,3,4,6,7,12,12, a-octahydropyrazino[2′,1&prime:6,1] Pyrido [3,4-b] Indole [centbutindole]: A Potent Nuroleptic Drug

SAMRIDDHI A Journal of Physical Sciences Engineering and Technology ◽

10.18090/samriddhi.v3i1.1609 ◽

2015 ◽

Vol 3 (1) ◽

Author(s):

D. B. Singh ◽

Abadur-Rahman ◽

V. N. Shukla ◽

Vikash Kumar ◽

Pragya Gupta

Keyword(s):

Force Field ◽

Normal Mode ◽

Title Compound ◽

Normal Mode Analysis ◽

Mode Analysis ◽

X Ray Diffraction ◽

Vibrational Dynamics ◽

5Ht2 Receptors ◽

Gross Behavior ◽

Good Agreement

FITR spectra and normal mode analysis of compound 2-[3-(p-flourobenzoyl)propyl]-1,2,3,4,6,7,12,12, a-octahydropyrazino[2′,1′:6,1] pyrido [3,4-b] indole [centbutindole], which is a potent nuroleptic drug and belong to a series of 2-substituted pyrazino-pyrido indoles. It also blind with 5HT2 receptors. It has shown good antihypotensive activity. The well known Wilson’s G-F matrix method with Urey-Bradely force field has been used to evaluate the normal mode frequencies of vibration. Good agreement has been obtain between them and a set of 29 force field constants is established. The vibrational dynamics of the title compound is being reported using Urey Bradley force field. It has shown acute toxicity, gross behavior and central effects like anti convulsant activity, anti reserpine activity and stereo specificity of action. The conformation of the title compound was determined by X-ray diffraction. It is planned to determine the conformation in such cases by the application of Fourier Transform Infrared (FITR) spectroscopy and normal mode analysis. As a first step in this direction the FITR spectrum of the title compound has been recorded and its normal mode analysis is carried out. The assignments of the frequencies are based on the theoretically calculated frequencies have also been given their best assignment.

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