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 Files

  • 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.

Video Tutorials

FAQ

Disclaimer

ALL PLANS AND SOFTWARE DISTRIBUTED HERE ARE OFFERED ON AN AS-IS BASIS. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

Share |