Training
Previous Workshops
AMBER Workshop
2 - 3 September 2004, Imperial College London
The EPSRC National Service for Computational Chemistry Software held a two-day training workshop on the software package AMBER. The workshop was held in the Chemistry Department at Imperial College London on the 2nd and 3rd September 2004. The workshop was be given by Dr. Ian Gould (Imperial College London) and Dr. Ross Walker - The Scripps Research Institute.
AMBER is a computer program for applying molecular mechanics, molecular dynamics and free energy calculations to simulate biomolecules.The workshop consisted of a series of short lectures followed by hands on lab sessions that covered use of the AMBERmolecular dynamics software suite (http://amber.scripps.edu) and the theory behind it.
Specific topics covered include:
An introduction to modelling; basic equilibrium statistical mechanics and the principles of classical molecular dynamics including minimisation and dynamics algorithms, temperature regulation, pressure regulation and periodic boundary methods; implicit and explicit solvation models; the limitations of using a classical approach.
An introduction to each of the modules that make up the AMBER software suite, and a description of each of the different parameter sets available, the pros and cons of each and where to obtain help.
"Simple" peptide, protein and nucleic acid simulations including how to obtain a starting structure, creating prmtop and inpcrd files, running minimisations, gas phase and implicit solvent molecular dynamics, and how to view and analyse the results.
More advanced simulations of co-enzyme containing proteins and pharmaceutical compounds that require explicit parameters; how to create your own residues, including charge derivation and parameter selection.
An introduction to QM/MM coupled potential simulations.
Tutors:
Dr. Ian Gould - Imperial College London
Dr. Ross Walker - The Scripps Research Institute
Further information about AMBER can be found at the AMBER web site.
Photos from the workshop:
Dr Ross Walker (left) & Dr Ian Gould (right) getting ready for the start of the workshop |
Everyone working hard during the hands-on session |
Everyone tackling the tutopials |
Ross helping a workshop attendee |
Salinthip Thipayang helping out at the workshop |
Coffee break |
A chance to socialise |
Back to work again |
Tea break in the afternoon |
Relaxing with refreshments |
Making the most of the break before heading back for more hands-on session |
Having tea with biscuits |
