Simulaid: simulation setup and analysis utilites

Last updated: 01/12/2017
M. Mezei, J. Comp. Chem., 31, 2658-2668 (2010). DOI:10.1002/jcc.21551

Licensing/Downloading Information Full documentation
Commercial licence Download distribution

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  

Simulaid can perform the following operations:

List of other programs

Back to the Mezei Lab home page