Macrodox Tutorials v3.2.1
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Tutorial 1: An example tutorial session which reads in a Protein Data Bank file for the protein yeast iso-1-cytochrome c (1ycc) and assigns the charges to every atom based on a Tanford-Kirkwood calculation at a specified pH, temperature and ionic strength.
- Tutorial 2: Begins with the MDX file generated in the first
tutorial session for yeast iso-1-cytochrome c, where we properly assigned
its charges. Here we will calculate electrostatic fields around the protein
and calculate its solvent accessible surface exposures.
- Tutorial 3: Prepares a second species which will react with 1ycc in a robust Brownian dynamics simulation. In tutorial sessions 1 & 2 we prepared a molecule 1ycc in its Fe(III) oxidation state. This will be MOLECULE I in the BD scheme of things. We now prepare the partner for this to react with. The partner will be 1ycc in its Fe(II) state, so that we are to look at electron transfer self-exchange.
- Tutorial 4: Set up to run a robust Brownian dynamics
simulation which uses the BD program 'bdtirm8'. In tutorial sessions
1 and 2 we have prepared a molecule 1ycc in its Fe(III) oxidation state.
In session 3 we prepared 1ycc.fe2, a species in Fe(II) state. Here, we
must prepare two other files in order to run bdtirm8
- Tutorial 5 : In this tutorial, the command REVIEW is used to set up and run an analysis
in which a history file produced by a BD simulation is read in and the
complexes saved in the history file are reconstructed and analyzed.
MacroDox has been co-authored by:
Dr. Scott H. Northrup, George P. Stevenson, Theo L. Laughner, Andy Boswell and Kiran Mukhyala
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