Podcast
Questions and Answers
What is a limitation of the MM3 force field with regard to vibrational spectra?
What is a limitation of the MM3 force field with regard to vibrational spectra?
- Rotational barriers are high
- Accurate prediction for highly saturated hydrocarbons
- Vibrational spectra are not accurately calculated (correct)
- Partial double bonds in saturated molecules
Which of the following is affected by hyperconjugation according to the text?
Which of the following is affected by hyperconjugation according to the text?
- Vibrational spectra of saturated hydrocarbons
- Rotational barriers for alkenes
- Improper torsion-torsion angles
- Bond length changes in conjugated molecules (correct)
What dependency does hyperconjugation have on bond characteristics in molecules?
What dependency does hyperconjugation have on bond characteristics in molecules?
- Inductive effect on molecular weight
- Bond length changes due to higher H+ character (correct)
- Higher stability in saturated hydrocarbons
- Lowering the rotational barriers
In CHARMM, what type of chemistry is focused on by Harvard Macromolecular Mechanics?
In CHARMM, what type of chemistry is focused on by Harvard Macromolecular Mechanics?
What is a limitation of the MM4 force field in relation to saturated hydrocarbons?
What is a limitation of the MM4 force field in relation to saturated hydrocarbons?
What type of force field parameter is used for electrostatic calculations?
What type of force field parameter is used for electrostatic calculations?
Which type of experiments are used for parametrization in proteins according to the text?
Which type of experiments are used for parametrization in proteins according to the text?
What module in AMBER is used for minimization, molecular dynamics, and NMR refinements?
What module in AMBER is used for minimization, molecular dynamics, and NMR refinements?
Which AMBER force field is generally recommended for proteins?
Which AMBER force field is generally recommended for proteins?
What does the Replica exchange calculations in force field parameterization allow?
What does the Replica exchange calculations in force field parameterization allow?
In which type of calculations are provisions made for handling NOESY intensities and proton chemical shifts?
In which type of calculations are provisions made for handling NOESY intensities and proton chemical shifts?
What is the force field that accounts for all atoms in the periodic table?
What is the force field that accounts for all atoms in the periodic table?
What type of potential is used to describe bond stretching in the UFF force field?
What type of potential is used to describe bond stretching in the UFF force field?
What is the term used to describe the electrostatic interaction between charged atoms in the UFF force field?
What is the term used to describe the electrostatic interaction between charged atoms in the UFF force field?
How many atom types are defined in the UFF force field?
How many atom types are defined in the UFF force field?
What type of torsion term is used in the UFF force field?
What type of torsion term is used in the UFF force field?
What is the primary focus of the CHARMM22 force field reoptimization mentioned in the text?
What is the primary focus of the CHARMM22 force field reoptimization mentioned in the text?
What aspect of the force field was specifically optimized for the TIP3P water model?
What aspect of the force field was specifically optimized for the TIP3P water model?
In what solvent was the stabilization of the B form of DNA observed during the simulation?
In what solvent was the stabilization of the B form of DNA observed during the simulation?
What are the major simulations conducted for further validation of the reoptimized force field?
What are the major simulations conducted for further validation of the reoptimized force field?
Which force field is specifically designed for all-atom simulations of proteins?
Which force field is specifically designed for all-atom simulations of proteins?
What was noted as a limitation in the CHARMM22 force field reoptimization according to the text?
What was noted as a limitation in the CHARMM22 force field reoptimization according to the text?
What improvement was made to the CMAP potential in the experiment described?
What improvement was made to the CMAP potential in the experiment described?
Which part of the backbone CMAP potential was corrected in the study?
Which part of the backbone CMAP potential was corrected in the study?
What aspect of the CHARMM22 Gly and Pro CMAPs was corrected?
What aspect of the CHARMM22 Gly and Pro CMAPs was corrected?
What was the main focus of the experiments conducted with Ala3, Ala5, Ala7, Val3, and Gly3?
What was the main focus of the experiments conducted with Ala3, Ala5, Ala7, Val3, and Gly3?
Which technique was used to validate the experiments?
Which technique was used to validate the experiments?
In what type of proteins did the MacKerell Group focus their study on, according to the text?
In what type of proteins did the MacKerell Group focus their study on, according to the text?
