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Two-Body Grid

Generates structures by rigid body translations and rotations of one structure about a second structure.


The Two-Body Grid module is accessible from the Simulate section of the main menu.

Basic Usage

The purpose of the module is to perform rigid body displacements of an input structure (molecule 2) about a second (fixed) structure (molecule 1). Resultant structures contain both molecules.


Screen Shots and Description of Input Fields

This example generate stuctures of the HIVintegrase/LEDGF complex. One half of the complex (red) consists of two HIVintegrase subunits and one LEDGF subunit and serves as the fixed reference structure. The second half of the complex (blue) is translated and rotated about the first half to form structures of the entire complex.

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Example output

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run_0.dcd.pdb contains the intial coordinates for the complex containing both molecule 1 and 2.

run_0.dcd contains trajectories of the entire complex in which molecule 2 is displaced around molecule 1 as defined in the Move Input Section.

grid_output.txt contains the COM positions (x,y,z) and angular values (thetax, thetay, thetaz) of molecule 2 for the accepted structures.

Advanced Input

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Excluded Residue Section

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Files Used and Created in Example

Reference(s) and Citations

SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints
J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger Comp. Phys. Comm. 183, 382-389 (2012).

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