Modeling Proteins and Nucleic Acids with Amber, VMD and the MMTSB Toolkit

June 9-12, 2005


  • National Center for Research Resources
  • PSC's Biomedical Initiative. An NIH Resource Center
  • NIH Research Resource for Multiscale Modeling Tools in Structural Biology


Pittsburgh Supercomputing Center (PSC)
Mellon Institute Building, Pittsburgh, PA

APPLICATION DEADLINE: April 25, 2005 Applications are no longer being accepted


This workshop will cover the theory and practice of biomolecular simulations using the Amber suite of programs.  The lectures will cover the use of molecular mechanics force fields, the theory of solvation effects, and the connections between simulations and thermodyanmic quantitites.  Hands-on exercises will show how both implicit solvent and explicit solvent simulations can be carried out, visualized, and critically examined; participants are urged to bring specific projects from their own labs to use as examples.  More advanced topics will include treating part of the system (such as an enzyme active site) as a quantum region; using free energy simulations to estimate thermodynamic quantities; and using the MMTSB toolkit to accelerate sampling and to organize large-scale conformational explorations.

Participants should have an understanding of physical chemistry at the undergraduate level, and be familiar with the basics of protein and/or nucleic acid struture and chemistry.  Basic familiarity with the UNIX or Linux operating systems will be helpful.  More information on the software to be used can be found at (Amber), (VMD), and (MMTSB)



Theory and Practice of Biomolecular Simulations
Molecular Mechanics Force Fields
Solvation Effects
Quantum Mechanical Molecular Mechanical Calculations
Free Energy Simulations
MMTSB Tools, Utilities, Amber interface/scripts

Dr. David A Case
Department of Molecular Biology, TPC6
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037

Dr. Michael Crowley
Department of Molecular Biology, TPC6
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037

Dr. Ross Walker
Department of Molecular Biology, TPC6
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037

Suggested Readings for this workshop will be supplied to accepted participants 1-2 weeks prior to the workshop.

"AMBER" -- refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 8, which is distributed by UCSF subject to a licensing agreement described below.

A good general overview of the Amber codes can be found in: D.A. Pearlman, D.A. Case, J.W. Caldwell, W.R. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comp. Phys. Commun. 91, 1-41 (1995).

An overview of the Amber protein force fields, and how they were developed, can be found in: J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young. Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256 (2001).

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Photo 2 High Resolution Image (10 MB)