Simulaid: simulation setup and analysis utilites Last updated: 12/13/2024 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 Recently added features Inertia plot for K-means and K-medoid clustering Helix property tables, correlation, NMA Spearman and Kendall Tau rank correlations too Translate while converting a trajectory Option to permute bond list from topology files Option to override Y axis scale in 1D plots Check for long/short bonds in a trajectory Check for unphysical features on a trajectory Check for ligand-ligand overlap Calculate SD corresponding to CV values Calculate orientational fluctuation of a domain Color code bond tracks by domains Change a dihedral angle Secondary structure segment and residue counts Translate/rotate individual molecules Enhanced selection for bond plots Rotate around an axis defined by two atoms Shift in a direction defined by two atoms Calculate intra molecular RMSD Convert a stack of PDB files to MODELs

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
  • Cluster atoms using their distances or cruster based on an input distance matrix
  • Calculate eigenvaules and eigenvectors of an intput matrix
  • 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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