Simulaid: simulation setup utilites

The operations Simulaid can perform are grouped into three classes:

• Geometry optimizations
  • GENERAL (e.g., orientational optimization, pack/unpack trajectories)
  • CONVERSION (among a variety of structure and trajectory files and a variety of naming conventions)
  • ANALYSIS (e.g., helix properties hydrogen-bonded bridges, pseudorotation angles, DSSP assignment, RMSD plots and maps)
  • A. GENERAL
    
    • Find optimal centering of a solute (finds the center of the smallest enclosing sphere of the solute)

      

    • Find optimal orientation of a solute in a cube or a rectangle (finds the orientation that results in the smallest enclosing cube or rectangle of the solute) - useful, e.g., for setting up Delphi or GCMC calculations.

    • Optimize orientation of a solute in a periodic box to maximize the smallest image-image distance. The periodic box can be

  rectangular	face-centered cubic	hexagonal prism	truncated octahedron	hexagonal close-packed	image file based

  • Cleanup operations (resequencing, adding chain ID when missing, sorting)
  • Trajectory - structure file conversions
    • Separate configurations into single files from aggregates
    • Unpack a trajectory into single files
    • Combine configurations into a trajectory
  • Editing conformations
    • Edit the inputted structure (delete selected atoms, residues, chains)
    • Rotate and/or translate the inputted structure
    • Modify (replace/add atoms) the inputted structure
    • Trim (eliminate) solvents outside spheres or periodic boxes
    • Transfer the coordinates from one structure to an other
    • Write a PDB file of the alpha carbons
    • Fix distorted waters (replace with canonical waters) (in the same position and orientation)
  • Generate structre-derived information
    • Extract sequence description in a variety of formats
    • Create a Charmm or Amber trajectory file from a sequence of configurations
    • Create a Grasp .crg file by extracting the charges from a set of RTF files
    • Generate a torsion list for Macromodel or MMC input
  • Animate a trajectory (SGI only)

• B. CONVERSIONS
  
  • Convert a structure among Charmm .CRD, Brookhaven PDB, Charmm PDB (different segid location), Autodock .pdbqs, InsightII .car, Macromodel/Xcluster .dat, MMC .slt, as well as some InsightII free formats.
  • Make atomnames conform to Brookhaven conventions (e.g., HH12 -> 2HH1)
  • Convert atom and residue names among Charmm, Amber, Gromos/Gromacs, Moil, ChemX, and PDB conventions
  • Change the order of atoms within a residue according to a template or RTF file
  • Generate MMC Monte Carlo input
  • Generate an Amsol input
  • Generate a Gaussian Oniom input
  • Generate a UHBD .dat file
  • Generate residue record(s) for Charmm RTF file; when input is in InsightII .car format then atom types will be converted to Charmm22 atomtypes using the algorithm and code from the program Intocham.
  • Convert a trajectory among Charmm, Amber, MMC, or Macromodel formats
    Protocol to convert a Charmm trajectory to Amber
  • Provide a description of input formats

• C. ANALYSIS (on single configurations or trajectories)

  CV map	DSSP plot	Ramachandran plot	2-D RMSD map	Proline kink analysis	Bond history plot

  • Topology/geometry analysis
    • Generate a list of 1-4 distances and torsion angles
    • Generate a list of functional groups and backbone atoms
    • Generate statistics on various types of bond lengths
  • Bond tracking
    • Generate a list of hydrogen bonds
    • Generate a list of hydrophobic bonds
    • Generate a list of salt bridges
    • Generate a list of heavy-atoms in contact
    • Generate a list of hydrogen-bonded bridges anchored at the solute
      For selected hydrogen bonds, salt bridges, hydrophobic bonds or heacy-atom contacts
      • Plot the history over a trajectory
      • Calculate correlations among them
      • Cluster the bonds based on their correlation
  • Calculate atomic properties
    • Calculate circular variances (novel tool for mapping macromolecular topography).
    • Generate hydropathy-labeled structures
    • Label a structure by the potential read from a Delphi map
  • Calculate molecular properties
    • Calculate solvation shell volume and interface volume (for multimolecular solutes)
    • Calculate principal axes and their evolution
    • Calculate the radius of gyration and the hydrodynamic radius and their evolution as well as dipole moments of the solute and the whole cell
  • RMSD calculations
    • Calculate RMSD wrt an input structure over a trajectory
    • Calculate 2-D RMSD map over a trajectory
    • Calculate cross RMSD map over a pair of trajectories; optionally match structures between the two trajectories
  • Distance calculations
    • Generate list of residues within threshold distances Calculate the distribution of distance between selcted pairs of atoms
    • Check a conformation for potentially unphysical distances
    • Adjacency matrix analysis of Schuyler et al.
  • Prepare a Ramachandran plot
  • Prepare dial plots for selected torsion angles
  • Perform the proline kink analysis of Visiers et al. as implemented in the program ProKink
  • Perform a variety of helix analyses (TRAJELIX)
  • Calculate pseudorotational angles
  • Calculate/plot DSSP Helix/Sheet assignments
  • Prepare circular variance map
  • Calculate correlation and covariance matrices over a trajectory
  • Tabulate selected data from the output of the energy partitioning script mm_pbsa.pl written for Amber; calculate correlations among selected properties.

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