MMTSB/CTBP Workshop Tutorials

Tutorials

The following list of tutorials have been prepared for the MMTSB/CTBP Summer Workshop "Molecular simulation and structure prediction using CHARMM, Amber, and the MMTSB Tool Set" (August 4 - August 7, 2009). Participants are urged to move through each tutorial on-line and/or download the complete, stand-alone tutorial file.

All atom modeling

Simulating proteins and peptides

  • CHARMM/MMTSB - C peptide from RNAse A (suggested day 1) Setting up and running a simulation of the RNAse A N-terminal peptide (RNAse A C-peptide) with CHARMM and the MMTSB Tool Set. This tutorial is a good place to start as it demonstrates how one can build, manipulate and solvate such systems beginning from a PDB structure.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • MMTSB Tool Set - Setup of complex system (suggested day 1) This tutorial shows how to prepare a protein-RNA complex system for simulation using the MMTSB Tool Set.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • CHARMM - Polarizable domain swapped protein G (suggested day 1) This tutorial builds on the previous and uses the MMTSB Tools and CHARMM to set-up and run a solvated molecular dynamics simulation of the domain swapping mutant of the B1 domain of Streptococcal protein G using the CHARMM polarizable protein force field.
    Download complete tutorial as a compressed (tar/gzipped) file.

    • Simulating nucleic acids

  • MMTSB Tool Set - DNA Simulations with Amber (suggested day 1) In this tutorial the MMTSB Tool Set is used to carry out and analyze simulations of DNA with Amber.
  • MMTSB Tool Set - DNA Simulations with CHARMM (optional day 1) In this tutorial the MMTSB Tool Set is used to carry out and analyze simulations of DNA with CHARMM.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • CHARMM - RNA and DNA decamer (optional day 1) This tutorial introduces you to building and manipulating DNA and RNA models in CHARMM using the current generation of CHARMM fixed charge force fields. Limited features of the MMTSB Tool Set are also utilized.
    Download complete tutorial as a compressed (tar/gzipped) file.
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    Simulations with NAMD

  • MMTSB Tool Set - Simulations with NAMD (suggested day 1) NAMD can be used with CHARMM input/output files to run long MD simulations on highly parallel machines. This tutorial shows how to use mdNAMD.pl to interface with NAMD for simple MD simulations.
    Download complete tutorial as a compressed (tar/gzipped) file.
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    Trajectory Analysis

  • MMTSB Tool Set - Analysis of CHARMM simulations (suggested day 2) In this tutorial you will learn how to use the MMTSB Tool Set to carry out and analyze simulations with CHARMM.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • CHARMM - Trajectory Analysis (suggested day 2) The objective of this tutorial is to introduce users to simple analyses of trajectories with CHARMM.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • MMTSB Tool Set - Ensemble analysis (suggested day 2) This tutorial explores the ensemble computing capabilities of the MMTSB Tool Set for analyzing MD trajectories. Clustering, scoring, ranking, and other types of analysis are introduced.
    Download complete tutorial as a compressed (tar/gzipped) file.

    • Handling drugs and ligands

  • Sustiva and HIV-RT (suggested day 2) This tutorial illustrates the use of antechamber to create a force field for an arbitrary organic molecule. As an example, we show how to create parameters for sustiva (an anti-AIDS drug), and illustrate how to set up a simulation with sustiva bound to HIV reverse transcriptase.
  • Optimizing parameters for new molecules using the CHARMM force field (optional day 3) The all atom CHARMM force fields continue to evolve and expand in the chemical functionality that is covered. This tutorial aims to provide the basic elements necessary to extend the force field to add new functionality.
    Download complete tutorial as a compressed (tar/gzipped) file.

    • Continuum electrostatics

    Poisson Boltzmann calculations

  • MMTSB Tool Set - Continuum electrostatics calculations (suggested day 2) In this tutorial you will learn how to run and use continuum dielectric electrostatic calculations using CHARMM through the MMTSB Tool Set.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • CHARMM - Poisson-Boltzmann EQuation Solver Tutorial (optional day 2) The objective of this tutorial is to introduce users to the PBEQ module in CHARMM to calculate the electrostatics potential by solving the Poisson-Boltzmann Equation using the finite-difference method. This tutorial complements the previous one, which does similar things through the MMTSB Tool Set.
    Download complete tutorial as a compressed (tar/gzipped) file.

    Generalized Born models

  • GBSW Tutorial (Example 1: suggested day 2) The objective of this tutorial is to demonstrate the use of the GBSW implicit solvent model with optimized parameters in CHARMM. GBSW stands for a generalized Born (GB) model with a simple smoothed SWitching function.
    Download complete tutorial as a compressed (tar/gzipped) file.

    Implicit Membranes

  • Simulations in Implicit Heterogeneous Dielectric Environments (suggested day 2) This tutorial illustrates how to setup and run a simulation of phospholamban in a heterogeneous dielectric environment as a model of a phospholipid bilayer.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • GBSW Membrane Tutorial (GBSW_Tutorial Examples 2, 3: optional day 2) The objective of this tutorial is to introduce users to the GBSW implicit solvent model in CHARMM. GBSW stands for a generalized Born (GB) model with a simple smoothed SWitching function. The example examined is phospholamban, a membrane bound peptide.
    Download complete tutorial as a compressed (tar/gzipped) file.

    MMPB/SA and MMGB/SA calculations

  • MMTSB Tool Set - MMPB/SA ensemble computing (suggested day 2) This tutorial explores the ensemble computing capabilities of the MMTSB Tool Set to carry out MMPB/SA and MMGB/SA calculations. The WW domain from Yes-associated protein (Yap), for which a structure has been reported in complex with a bound proline rich peptide, is used to estimate the binding energy using molecular dynamics and MM/GBSA binding energy estimates.
    Download complete tutorial as a compressed (tar/gzipped) file.

    • Enhanced sampling

    Replica exchange simulations

  • Peptide Folding with GB (suggested day 3) This tutorial illustrates how to fold an alpha-helical peptide with implicit solvent using replica exchange through the MMTSB Tool Set.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • Analysis of replica exchange simulations (This tutorial uses data from the above tutorial - suggested day 3) This tutorial will illustrate how to use the MMTSB Tool Set to analyze replica exchange simulations, including weighted-histogram analysis to obtain free energy maps.
  • Replica exchange umbrella sampling (suggested day 3) This tutorial illustrates how to study DNA base flipping using replica exchange umbrella sampling through the MMTSB Tool Set.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • De novo Peptide Folding in Membrane GB (optional day 3) This tutorial illustrates how to run implicit membrane GB with the MMTSB toolset on a cluster.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • REX/GB Refinement of NMR Structures (optional day 3) This tutorial illustrates how to use the replica exchange (REX) molecular dynamics (MD) simulation together with the GBSW implicit solvent to refine NMR structures.
    Download complete tutorial as a compressed (tar/gzipped) file.
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    Constant pH molecular dynamics

    Free energy perturbation and potentials of mean force

    Structure Prediction

    Structure prediction with MMTSB/CHARMM

  • Template-based protein structure prediction (suggested day 4) This tutorial illustrates how to use the MMTSB Tool Set to access a variety of tools for template-based protein structure prediction.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • Loop modeling (sugggested day 4) In this tutorial you will learn how to use Modeller in combination with the MMTSB Tool Set to perform loop modeling.
    Download complete tutorial as a compressed (tar/gzipped) file.
  • Ab initio protein structure prediction (optional day 4) In this tutorial you will learn how to use the MMTSB Tool Set to perform ab initio protein structure prediction with MONSSTER without using a template.
    Download complete tutorial as a compressed (tar/gzipped) file.
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    Coarse grained models

    Go models for protein folding

  • Coarse-grained models for protein folding studies (suggested day 4) CHARMM can be utilized not only for all atom simulations, but also to explore the physical consequences of dynamics and thermodynamcis arising from coarse-grained models. In this tutorial a simplified model of the protein that represents only the Cα positions (the so-called Go model) is used to illustrate how one can explore and understand current single molecule pulling experiments.
    Download complete tutorial as a compressed (tar/gzipped) file.

    Multi-resolution model approach to reaction paths

  • Integrating Multi-scale, Low Resolution Models With Atomistic Models (suggested day 4) This tutorial illustrates the use of the Normal Mode Flexible Fitting (NMFF) algorithm and the MMTSB Tool Set to generate atomically detailed pathways connecting the known initial and final conformations of the protein system adenylate kinase (a phosphate transfer enzyme that undergoes a large conformational change during functioning).
    Download complete tutorial as a compressed (tar/gzipped) file.

    • Hybrid QM/MM Simulations

    Running QM/MM simulations with AMBER

  • An introduction to running QM/MM simulations with AMBER.(suggested day 3) This tutorial illustrates how to run QM/MM simulations using AMBER v10 and the built in semi-empirical QM/MM functionality in this package.