Summer School 2009

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Molecular Simulation and Structure Prediction using

CHARMM and the MMTSB Tool Set

August 4-7, 2009 at UCSD campus in La Jolla, CA

1 Information & Update
2 Housing, Meals & Travel Information
3 Schedule
4 Computer Lab Instructions

Information & Update

The Summer school participants can use this wiki page for any feedback, questions, suggestions, etc.

Housing, Meals & Travel Information

Schedule

Summer School Schedule (PDF)

Tuesday, August 4: Introduction, AMBER & MMTSB

Morning Session - Lectures (Humanities & Social Sciences (HSS) Building, Room 1330)

8:30 - 9:45 AM - Charles L. Brooks, III – Welcome, historical overview and introduction to molecular mechanics and modeling with CHARMM and the MMTSB Tool Set
- Welcome and overview of MMTSB and CTBP objectives
- Introduce CHARMM, Amber and the MMTSB Tool Set with a historical perspective
- A brief overview of methods in molecular modeling – nature of force field, minimization and molecular dynamics, introduction to periodic boundary conditions
- A brief introduction to the flow of CHARMM calculations
- Comments on scope and range of problems that can be addressed with CHARMM.
- The nature of the CHARMM force field, molecular fragments and parameterization strategies
9:45 - 10:00 AM - Coffee Break
10:00 - 11:00 AM - David Case – The Amber program suite for simulations of molecular systems
- Introduce Amber with an historical perspective
- A brief introduction to the flow of Amber calculations
- Comments on scope and range of problems that can be addressed with Amber
- The nature of the Amber force field, molecular fragments and parameterization strategies
11:00 - 12:00 PM - Michael Feig - Introduction to MMTSB scope and functionality
12:00 PM - 2:00 PM - Lunch

Afternoon Session - Tutorials (Natural Sciences Building (NSB), Room 1205)

2 - 5 PM - Tutorials/Hands-On Session - Elementary applications to peptides, proteins and nucleic acids (Brooks, Case, WAlker, Feig and mentors)
- Brooks/Feig
  - Visualizing molecules and trajectories with VMD. (VMD Tutorial)
  - Building, minimizing and solvating an a-helical peptide – C-peptide from RNAse A. (RNAase A/C-peptide CHARMM/MMTSB Tutorial)
  - Conditioning/preparing a multi-domain protein for simulation using the MMTSB Tools. (MMTSB setup)
- Case/Walker
  - Conditioning/preparing DNA for molecular dynamics
    - with Amber DNA/RNA force fields
    - using MMTSB Tools to run an ADNA --> B-DNA transition
    - application of MM-GBSA to protein-protein and protein-DNA complexes
    - use of W3DNA (http://w3dna.rutgers.edu) to build DNA starting structures

7-10 PM - Reception & mini-poster session. (Middle Earth Lounge, ERC Housing Complex) Refreshments will be served.

Wednesday, August 5: CHARMM

Morning Session - Lectures (1330 HSS)

8:30 - 9:30 AM - Jianhan Chen - CHARMM analysis tools and facilities
- Overview of CHARMM analysis facilities, trajectory analysis, NMR module
- Illustrative examples of solvent analysis, hydrogen bonding, clustering w/ K-means cluster facility
9:30 - 9:45 AM - Coffee Break
9:45 - 11:00 - Jianhan Chen/David Case - Implicit solvent models in CHARMM and Amber
- Overview of CHARMM empirical implicit solvent models (ASA, EFF,IMFF)
- Continuum solvent models in CHARMM (PB, GB)
- Overview of GB and Amber empirical implicit solvent models
11:00 AM - 12:00 PM - Sishi Tang - Introduction to AMBER"s Antechamber and the General AMBER Force Field
- Overview of General AMBER FOrce Field. Antechamber, automayed atom type parameter selection for ligands
- Examples of combining GAFF with protein force fields (FF99SB)
- Problematic systems to be aware of
12:00 PM - 2:00 PM - Lunch

Afternoon Session - Tutorials (1205 NSB)

2 - 5 PM - Tutorials/Hands-On Computer Session - Applications to membrane/protein systems, implicit solvent simulations and trajectory analysis. Use of AMBERS's Antchanber module (Jianhan Chen, Michael Feig, David Case, Ross Walker and mentors)

Chen/Feig
- Basic analysis of MD trajectories with MMTSB Tool Set (MMTSB Trajectory analysis)
- Advanced trajectory analysis with CHARMM (CHARMM Trajectory analysis)
  - Comparative analysis of protein structures (e.g., rmsd versus reference, hydrogen bonding, secondary structure)
  - Examples of analysis of solvent/solvation structure and dynamics
  - Clustering molecular trajectories based on backbone conformations
- Ensemble analysis and clustering with MMTSB Tool Set (Ensemble analysis)
Case/Tang/Walker
- Use of Antechamber for modeling pharmaceutical compounds with AMBER
- GB Simulations of proteins and nucleic acids with AMBER
Feig
- Optimized GBSW simulations with CHARMM/MMTSB (GBSW model)
- Implicit membrane simulations with CHARMM/MMTSB (HDGB model)
- Poisson-Boltzmann calculations with CHARMM/MMTSB (MMTSB PB calculations)
- MMPB/SA type analysis (using MMTSB ToolSet ensemble tools). (MMPB/SA ensemble computing)

Thursday, August 6: CHARMM / MMTSB

Morning Session - Lectures (1330 HSS)

8:30 - 9:30 AM - Jianhan Chen - Replica-exchange molecular simulations with CHARMM and MMTS
- Theoretical background of replica exchange MD
- Illustrative examples for membrane assembly, peptide folding and protein refinement
- Using umbrella sampling, WHAM analysis (w/Feig)
9:30 - 9:45 AM - Coffee Break
9:45 - 10:45 AM - Jana Sen - Constant pH molecular dynamics with CPHMD
10:45 - 11:45 AM - Ross Walker - QM/MM Simulations in Amber
11:45 AM - 2:00 PM - Lunch

Afternoon Session - Tutorials (1205 NSB)

2 - 5 PM - Tutorials/Hands-On Computer Session - Replica exchange, constant pH and QM/MM (Shen, Feig, Walker and mentors)

Chen/Feig
- Temperature replica exchange simulations (Replica exchange folding)
- WHAM analysis, construction of PMFs (Replica exchange analysis)
- Replica exchange umbrella sampling (Umbrella replica exchange)
Shen
- Constant pH molecular dynamics tutorial
Walker
- Amber QM/MM tutorial

Friday, August 7: Simulation & Modeling

Morning Session - Lectures (1330 HSS)

8:30 - 9:30 AM - Michael Feig - Using the MMTSB Tool Set with Modeller and CHARMM for protein structure prediction
- Overview of structure prediction capabilities
- Applications from homology/loop modeling to de novo structure prediction
9:30 - 9:45 AM - Coffee Break
9:45 - 10:45 AM - Charles Brooks, III - Developing and implementing multi-resolution models with CHARMM
- Topological and flavored Go models for the investigation of protein folding and unfolding.
- Multi-scale RNA models for RNA structure and thermodynamics
10:45 - 11:45 AM - David Case - Free energy simulations in Amber
11:45 - 2:00 PM - Lunch

Afternoon Session - Tutorials (1205 NSB)

2 - 5 PM - Tutorials/Hands-On Computer Session - Structure prediction, multi-scale, multi-resolution modeling, free energy (Brooks, Case, Feig)

Feig
- Template-based structure prediction (Template predictions)
  - Secondary structure prediction through psipred
  - Sequence alignment through PSI-BLAST
  - Homology modeling through the MMTSB Tool Set
- Loop modeling with Modeller and MMTSB Tool Set (Loop modeling)
- Brooks
  - Using CHARMM and MMTSB to explore protein folding mechanism and thermodynamics
  - Exploring single molecule protein pulling experiments with Go models
- Case
  - Amber free energy tutorial

Workshop Ends at 5 PM

The workshop organizers wish to acknowledge the support of the National Science Foundation Physics Frontiers Centers program and the National Institutes of Health National Center for Research Resources program.