This example performs molecular Monte Carlo (MC) simulations on Single-Stranded nucleic acid to generate many structural configurations of rpoS messenger ribonucleic acid (mRNA).
The starting structure must be a complete structure without missing residues. Atom and residue naming must be compatible with those defined in the CHARMM force field. See the pages on Structures and Force Fields and PDB Scan for further details.
Structures are generated by Markov Monte Carlo sampling of single-stranded nucleic acid backbone torsion angles. Energetics of the torsion angles are determined using CHARMM force field parameters.
run name user defined folder name for storing the results.
reference pdb PDB file with atomic information and coordinates for the starting structure.
PSF Filename PSF file with topology information, must match the reference PDB file.
output file name Name of output DCD file containing the accepted structures.
number of trial attempts Number of Monte Carlo moves to attempt.
return to previous structure After this number of Monte Carlo moves fails to find an accepted configuration, re-load a previously accepted structure. If this value is set to 1, any failed step will backup to the previous configuration then attempt a new Monte Carlo move. For values greater than 1, a random structure form the previously accepted structures is selected. When the simulated system contains B-DNA, typically users should use a value of 1 to explore large variations from the starting configuration. If you think of the Monte Carlo simulation as a walk with the initial configuration as the starting location, a value of 1 would represent continuously walking away from that starting location, while a value greater than 1 would represent repeatedly returning to locations previously visited. The first option will typically be the quickest method for exploring configurations far from the starting structure, while the later option will more thoroughly explore configurations around the starting point.
temperature (K) Simulation temperature use for calculating energies from CHARMM force field parameters and calculating the screened Debye electrostatic energy.
number of flexible regions to vary An integer value indicating the number of regions to sample torsions. The value entered will dictate the number of further inputs to be created.
move direction This parameter applies to protein backbone, single-stranded nucleic acid (ssNA), and isopeptide bond torsions, but does not apply to B-DNA moves (the page on B-DNA directionality explains how to define the move direction for B-DNA). For protein and ssNA systems, forward and reverse respectively indicate that the moved residues will be those with a resid larger and smaller than those in the flexible region. For isopeptide systems, forward and reverse respectively indicate the moved residues will be those on the lysine and C-terminal sides of the isopeptide bond. The selected option must match the selection defined in the post region input.
flexible region Unique descriptor to define each flexible region (VMD like input).
post region Unique descriptor to define each flexible region (VMD like input).
max theta Maximum angle, in degrees, to sample in a single MC move. This input is specific to each region. The default values for protein and B-DNA are respectively 30 and 10 degrees. These values typically provide both a reasonable amount of both variation and acceptance.
overlap basis Select the basis atoms used in determining overlap. Available options are:
The notation used for defining flexible and post regions follows the notation used in VMD (this does not include shortcuts and generic options such as 'backbone', 'sidechain', 'nucleic', 'water', 'protein', etc). As a general rule, do not include the first or last residue of a segment in a flexible region.
Illustration of the starting structure. The rigid protein and RNA are respectively colored blue and red. The flexible and post regions are respectively highlighted using yellow and white. The input definitions for this selection is as follows:
flexible region:
segname RNA1 and resid > 127 and resid < 130post region:
segname RNA1 and resid > 129
The output will indicate the location of the output files, acceptance and overlap statistics, and the file names of the inputs, log, and output DCD. Results are written to a new directory within the given "run name" as noted in the output. In addition, a plot of Rg versus structure number is shown (currently NOT implemented).
Several files are generated and saved to the <run name>/monte_carlo/ directory: a copy of the original input PDB and PSF files, the output DCD file containing accepted structures, a PDB and PSF file for each group, flexible region, and post region, the json inputs, and a log file. In this example, the dcd containing the generated structures accepted by the Monte Carlo algorithm is one_ssna_flex/monte_carlo/rna_protein_complex.dcd.
input files
output files
| Protein Backbone | B-DNA | Single-Stranded Nucleic Acid Backbone | Isopeptide Bond | |
|---|---|---|---|---|
| HIV-1 Gag Matrix Protein | X | |||
| Full HIV-1 Gag Protein | X | |||
| Diubiquitin | X | |||
| rpoS mRNA | X | |||
| Linear strand of B-DNA | X | |||
| Nucleosome Core Particle | X | X | ||
| Tetranucleosome | X | X |