Tool Set Documentation

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Common applications of the MMTSB toolset

Helpful hints for using the MMTSB toolset in projects


Structure preparation conversion/manipulation of PDB files completion of missing atoms amino acid residue mutations nucleotide base mutations

Structure analysis center of mass center of mass radius of gyration root mean square displacement least-squares fit superposition identification and comparison of native contacts contacts between different chains minimum distance between two residues Q-score calculation phi/psi/chi1 dihedral calculation identification of residues within cutoff clustering based on mutual similarity

All-Atom Modeling evaluate energy with CHARMM minimize with CHARMM run molecular dynamics with CHARMM analyze molecular dynamics simulations with CHARMM normal mode analysis with CHARMM Poisson-Boltzmann calculations with CHARMM explicit solvent simulations equilibration obtain scalar variables from CHARMM generate PSF file from PDB generate DCD trajectory from list of PDBs process DCD trajectory file evaluate energy with Amber minimize with Amber run molecular dynamics simulation with Amber run molecular dynamics simulation with NAMD

SICHO Lattice Modeling SICHO lattice simulation with MONSSTER SICHO energy from MONSSTER generate lattice chain from PDB rebuild all-atom model from lattice chain check validity of lattice chain generate MONSSTER sequence file generate MONSSTER input file generate MONSSTER restraint file extract lattice chain from MONSSTER trajectory multi-scale lattice/all-atom sampling

Replica Exchange Sampling all-atom replica exchange simulation with CHARMM all-atom replica exchange simulation with Amber lattice replica exchange simulation with MONSSTER GO model replica exchange simulation with CHARMM multi-scale lattice/all-atom replica exchange simulation) replica exchange control information replica exchange analysis read replica exchange trajectory archive file write replica exchange trajectory archive file replica exchange server

Ensemble Computing generate ensemble from PDB files run command across ensemble minimize ensemble structures evaluate energy for members of ensemble generate ensemble from lattice simulations truncate residues of all members of ensemble obtain list of files for ensemble structures obtain data items for ensemble structures set data items for ensemble structures calculate standard structural properties for ensemble cluster ensemble structures rank clusters display clusters start job server for parallel runs

Structure Prediction build template-based model with loops generated by MODELLER model loops with MODELLER predict secondary structure with PSIPRED obtain sequence alignment with PSI-BLAST