Simulaid: simulation setup and analysis utilites Last updated: 07/29/2022 M. Mezei, J. Comp. Chem., 31, 2658-2668 (2010). DOI:10.1002/jcc.21551 Licensing/Downloading Information Full documentation Commercial licence Download distribution Examples/tutorials Features added after the publication of the paper Generate crystal unit cell, biological dimer from asymmetric unit Cluster and subcluster based on input data (e.g., Tanimoto similarity matrix) Separate a GCE trajectory into Amber trajectories Extract cluster center structures after clustering Read charges from Charmm or Amber topology file or Autodock .pdbqt file Calculate and plot the difference between residue distance matrices and residue RMSFs Calculate and plot the difference between bond (hydrogen/hydrophobic bond; salt bridge) matrices Individualize atom names, scale coordinates, save mol2 file with names or coordinates changed Allow atom selection by atom or residue names; generate plot of atom-atom distance SDs Support for Tripos .mol2 (mostly for input) and Maestro .mae (only for input) formats Rotate a molecule based on a bond direction Calculate intermolecular distance matrix Concatenate atom-atom bond histories to residue-residue bond histories Calculate bond state statistics and autocorrelations Draw bonds between (anti)correlated bonds Heuristic clustering into cliques Density-based clusterings Helix analysis (TRAJHELIX) on several helices Filter solvents by proximity, CV or interface Align a molecule's principal axes to the XYZ axes Calculate angle distributions with dial plots Calculate two kinds of helix-helix distances, and helix rotations relative to other helices Filter for solvents forming H-bond bridges Bond tracks for mutually proximal atom pairs Residue-residue autocorrelation (lifetime) Swap chirality Input of PDBx/mmCIF files Convert sequence files Read bond list from RTF or top files; print MMC MAKB or PDB CONECT records Specify atom lists for molecular overlay Filter trajectories/structures for energy Plot and cluster torsion angle circular correlation matrix, calculate its eigenvectors, eigenvalues Create a PDB file of a rectangle (box/cube) Calculate RMSD for residues Process clusters with user-defined limits; use even-spaced or random intial trys for clustering Create periodic replica cells Plot PBC cell sizes, volume Track solvent diffusion, membrane transit Principal axes by domains, angle between them Average data in 1D plots Calculate membrane deviation from flatness Inertia plot for K-means and K-medoid clustering

Simulaid can perform the following operations:

• A. GENERAL
  
  • Log all keyboard input
  • 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

  • Eliminate solvents outside spheres or periodic boxes
  • Replace distorted waters with canonical waters (in the same position and orientation)
  • Scale, rotate and/or translate the inputted structure
  • Edit (remove/add atoms) the inputted structure
  • Separate configurations into single files from aggregates
  • Unpack a trajectory into single files
  • 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 crystal unit cell from the asymmetric unit
  • Generate a (putative) biological dimer from the asymmetric unit
  • Generate a list of asymmetric unit contacts
  • Generate a torsion list for Macromodel or MMC input
  • Print a PDB file of unit cell vertices and neighboring unit cells for different PBC cell shapes
  • Cleanup operations (resequencing, adding chain ID when missing, sorting)

• B. CONVERSIONS
  
  • Provide a description of various structure file formats
  • Convert a structure among Charmm .CRD, Brookhaven PDB, Charmm PDB (different segid location), InsightII .car (from Accelrys), Macromodel/Xcluster .dat, MMC .slt, as well as some InsightII free formats; or from Tripos .mol2 format.
  • 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
  • Convert a trajectory to Charmm, Amber, Macromodel, or MMC binary format; structure can be rearranged, centered and/or filtered during the conversion. Click HERE for the detailed protocol of Charmm - Amber trajectory conversion.

• C. MODIFY structures
  • Delete/change selected atoms
  • Add new atoms defined by bond, angle and torsion
  • Translate/rotate/scale; center in a PBC sell
  • Separate molecules
  • Swap chirality
  • Permute coordinates
  • Swap coordinates
  • Overlay on a different structure

• D. ANALYSIS (on single configurations or trajectories)

  CV map	DSSP plot	Ramachandran plot	2-D RMSD map
  Proline kink analysis	Torsion angle dial plot	Hydrogen-bond history	Bond stat/correlation

  • Generate a list of hydrogen bonds
  • Generate a list of hydrogen-bonded bridges anchored at the solute
  • Generate a list of functional groups and backbone atoms
  • Generate a list of 1-4 distances and torsion angles
  • Generate statistics on various types of bond lengths
  • Generate list of residues within threshold distances
  • Plot the difference between residue contact lists
  • Check a conformation for potentially unphysical distances
  • Perform the proline kink analysis (ProKink) of Visiers et al.
  • Calculate circular variances and circular variance maps (novel tools for mapping macromolecular topography).
  • Generate hydropathy-labeled structures
  • Calculate pseudorotational angles
  • Calculate/plot DSSP Helix/Sheet assignments
  • Prepare Ramachandran plots
  • Calculate solvation shell volume
  • Calculate radius of gyration and hydrodynamic radius
  • Calculate principal axes
  • Calculate 2-D RMSD map and cross RMSD map (with or without superimposition)
  • Calculate average B-factors
  • Calculate residue adjacency power matrix
  • Calculate correlation and covariance matrices over a trajectory
  • Calculate atom-atom distance SD matrix (sigma-r plot) from a trajectory
  • Perform a variety of helix analyses (TRAJELIX) on a single helix or on several helices
  • Cluster trajectory based on the 2-D RMSD map
  • Cluster atoms based on their Cartesian distance
  • Cluster and subcluster based on input data (e.g., Tanimoto similarity matrix)
  • Plot the history and average of different types of "bonds" (hydrogen bond, hydrophobic contact, salt bridge); cluster the bonds
  • Plot the difference between averages for these different types of "bonds"
  • Extract and summarize parts of Amber energy decomposition tables
  • Create a PDB file for various PBC cell vertices and for image cell centers for various PBCs

List of other programs

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