The following list of tutorials were prepared for the MMTSB/CTBP Summer Workshop "Molecular simulation and structure prediction using CHARMM and the MMTSB Tool Set" (July 31 - August 4, 2006). 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

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 explores both all atom fixed charge and polarizable force fields (with the CHARMM charge equilibraiton force field for proteins) and illustrates how one can build, manipulate and solvate such systems beginning from a pdb file. This tutorial is a good place to start. Download complete tutorial as a compressed (tar/gzipped) file.

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 simulaiton 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

RNA and DNA decamer (suggested day 1) This tutorial introduces you to building and manipulating DNA and RNA models in CHARMM using the current generation of CHARMM fixed charge firce fields. Limited features of the MMTSB Tool Set are also utilized. Download complete tutorial as a compressed (tar/gzipped) file.

Nucleic acids with the polarizability (suggested day 2) An alternative force field with polarizability, the Drude force field, is illustrated for simulations of DNA. This tutorial builds on the previous. While the Drude model is not yet fuly available for inclusion of polarizability, this example illustrates the basic elements involved in carrying-out simulaitons with atomic polarizibility based on the Drude oscillator model. Download complete tutorial as a compressed (tar/gzipped) file.

CHARMM Analysis Facilities

Trajectory Analysis Tutorial (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.

Simulating membrane systems

Membrane Builder Tutorial (suggested day 2) In this tutorial you will be introduced to a step-by-step procedure to build a membrane system with CHARMM. Download complete tutorial as a compressed (tar/gzipped) file.

GBSW Membrane Tutorial (suggested 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.

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.

Using the MMTSB Tools for all atom calculations

MMTSB Tool Set - Initial Setup (suggested day 1) This tutorial is directed toward learning how to perform basic manipulations with the MMTSB Tools to prepare a system for simulaiton. In this example we consider a protein-RNA complex. Download complete tutorial as a compressed (tar/gzipped) file.

MMTSB Tool Set - Simulations with CHARMM (suggested day 1) In this tutorial is you 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.

MMTSB Tool Set - DNA Simulations with CHARMM (suggested day 2) 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.

De novo Peptide Folding in Membrane GB (suggested day 2) 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.

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.

All atom force fields

Adding new molecules to the CHARMM force field (suggested 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.

Using the Merck Molecular Force Field in CHARMM (suggested day 3) CHARMM supports many force fields. One that is particularly useful in molecular modeling studies of drug like molecules is the Merck Molecular Force Field, developed by Tom Halgren and his colleagues at Merck. This tutorial demonstrated how one can use this force field to study the interactions between a ligand and protein. The protein is represented with the CHARMM all atom force field and the ligand with MMFF. Download complete tutorial as a compressed (tar/gzipped) file.

Refinement of NMR structures using CHARMM and the MMTSB Tool Set

REX/GB Refinement of NMR Structures (suggested 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.

Continuum electrostatics

Generalized Born and 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.

Poisson-Boltzmann EQuation Solver Tutorial (suggested 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.

Free energy methods

Free energy perturbation and potentials of mean force

MMTSB Tool Set - Ensemble computing (suggested day 4) This tutorial explores the ensemble computing capabilities of the MMTSB Tool Set. 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.

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.

Ab initio protein structure prediction (suggested day 4) In this tutorial is you 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.

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 (an phosphate transfer enzyme that undergos a large conformaitonal change furing funcitoning). Download complete tutorial as a compressed (tar/gzipped) file.