Molecular Mechanics and Dynamics Characterization of an In Silico Mutated Protein
A Stand-Alone Lab Module or Support Activity for In Vivo and In Vitro Analyses of Targeted Proteins
This page contains the supplemental information for the article
"Molecular Mechanics and Dynamics Characterization of an In Silico Mutated Protein: A Stand-Alone Lab Module or Support Activity for In Vivo and In Vitro Analyses of Targeted Proteins," Harry Chiang, Lucy C. Robinson, Cynthia J. Brame, and Troy C. Messina, Biochemistry and Molecular Biology Education, submitted April 2013.
Please reference this manuscript for any publications containing results using this apparatus or derivatives of it. By downloading any of the materials, you are agreeing to our disclaimer (see below).
- Supplemental PowerPoint - File for display in class to assist with the lab.
- psfgen.pgn - Sample pgn file for mutation to phosphoserine. File names will need to be altered. This process may be carried out in the AutoPSFGenerator.
- Water sphere tcl
- namdstats.tcl - File for calculating statistics such as energy of each timestep in a minimization.
- distance.tcl - File for calculating distances between selections of atoms.
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