NykkiPS7_2018.doc - Name_Nykki Ogbomoh Molecular Modeling...

This preview shows 1 out of 3 pages.

Name: __________ _Nykki Ogbomoh________________________ Molecular Modeling Chem 4450/6450 Fall 2018 Set 7 Due on 11/1 1) Dynamics: Ouabagenin (Maestro/Macromodel) (75 points) Below find the heteroatom skeleton of these molecules ( file provided) . You must use the file called OuabageninB and OuabageninC. As it turns out (previous homework) the molecule can exist in two stable conformations differing in the conformation of the 6 membered ring on the right. a) Run an MD run (50ps) on the boat form at 400K. Molecular dynamics FF = mm3*, charges = from FF. Dielectric = 1, constant, no solvent, shake = bound to H , Before you start the dynamics minimize the structure thoroughly using mm3* (PRCG, Grad 0.01) REPORT ENERGY. Boat: 251.167 kJ/mol Chair: 216.171 kJ/mol 5 50ps, 2fs step, 50 snaphots (do not minimize), T=400, Monitor the characteristic distances and couplings 1) (see previous homework). What is happening? Make a plot of the energy (E pot, temp vs time) 20
Image of page 1

Subscribe to view the full document.

Make plots of the distances and torsions (every ps) 10 Plot of RMSD during simulation 10 Which of the rings changed, just one or is there more to this? 5 Only boat ring changed to chair after 20 or little more ps b)
Image of page 2
Image of page 3
You've reached the end of this preview.
  • Spring '14
  • DonaldHamelberg
  • Molecule, Disulfide bond, Epot, MD run

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern