C7800 Introduction to molecular modelling - exercise -1Section
Modelling
Programs for molecular modelling I
Petr Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kotlářská 2, CZ-61137 Brno
C7800 Introduction to molecular
modelling - exercise
TSM Modeling of molecular structures
C7800 Introduction to molecular modelling - exercise -2-
Overview
VMD
http: //www.ks.uiuc.edu/Research/vmd/
Visualization of (bio)molecules. Available for MS Windows, macOS, and Linux for
free upon registration.
Avogadro
http://avogadro.openmolecules.net/wiki/Main_Page
Program for molecule building and visualization. Freely available for MS
Windows, macOS, and Linux.
Functionality overview: https://www.youtube.com/watch?v=xdmLoBlLmqs
Nemesis
https://nemesis.ncbr.muni.cz/
Program for molecule building and visualization. Freely available for Linux.
C7800 Introduction to molecular modelling - exercise -3WOLF
Cluster - GNOME Desktop
Settings,
logout, shutdown
Standard
applications
Dock
(running applications,
frequently used
applications)
Terminal type "terminal"
C7800 Introduction to molecular modelling - exercise -4Model
building
Program Avogadro
C7800 Introduction to molecular modelling - exercise -5How
to start Avogadro?
▪ Find Avogadro in standard applications
▪ Or open terminal and run Avogadro as a command (all small caps!!!)
▪ Or open terminal and run Avogadro from modules (not recommended)
Starting Avogadro
$ avogadro
$ module add avogadro
$ avogadro
C7800 Introduction to molecular modelling - exercise -6Draft
model
• In edit mode, you can draft a model.
• This model does not have proper bond distances and angles. It needs to be
optimized before further use.
C7800 Introduction to molecular modelling - exercise -7Model
optimization
• Avogadro uses molecular mechanics (force field) for geometry optimization.
• For proper usage, the model must have correct topology with right bond
orders.
• Force field methods are empirical. Therefore, it is necessary to select proper
parametrization such as MMFF94.
C7800 Introduction to molecular modelling - exercise -8Exercise
1
1. Step by step, create models of the following molecules:
• methane
• ethene, ethyne
• benzene
• adamantane
• benzoic acid
• trinitrotoluene
• salicylic acid
• optionally building C60
C7800 Introduction to molecular modelling - exercise -9Exercise
2
1. Create a model containing G:C base pair, according to the scheme below. Use a
hydrogen atom to saturate the free valences. For geometry optimization, use the
MMFF94 force field.
https://en.wikipedia.org/wiki/Base_pair
C7800 Introduction to molecular modelling - exercise -10Model
building
Nemesis program
C7800 Introduction to molecular modelling - exercise -11How
to start Nemesis?
▪ Open terminal and run Nemesis from modules:
Starting Nemesis
$ module add nemesis
$ nemesis
C7800 Introduction to molecular modelling - exercise -12Nemesis
- Build Project
layers
graphic models
molecule building / editing
geometry measurement
Force field settings for optimization: menu Geometry-> Optimizer Setup
geometry optimization
using a force field
Mouse:
• left button - selection
• middle button - rotation
• right button - translation
• wheel - zoom
Keys:
•Shift - XY -> Z
•Ctrl - primary/secondary manipulator
C7800 Introduction to molecular modelling - exercise -13Exercise
3
1. Step by step, create models of the following molecules:
• methane
• ethene, ethyne
• benzene
• adamantane
• benzoic acid
• trinitrotoluene
• salicylic acid
C7800 Introduction to molecular modelling - exercise -14Visualization
of molecular
dynamics simulations
VMD program
C7800 Introduction to molecular modelling - exercise -15Exercise
4
molecular dynamic simulation of
a molecular switch
red - rotor
orange - axis
blue - water
C7800 Introduction to molecular modelling - exercise -16Display
simulation in VMD
$ ~kulhanek/start-vmd-3
▪ Open terminal and run the following script
C7800 Introduction to molecular modelling - exercise -17-
VMD
Representation
movement in time
C7800 Introduction to molecular modelling - exercise -18VMD
program - visualization
1 2
3
4
5
Create/Delete representation
Representation List
double click - activate/deactivate
Selection (what part of model is visualized)
Coloring method and drawing method
C7800 Introduction to molecular modelling - exercise -19VMD
program - selection
Selection for visualization (examples):
water - selects all water molecules
resname X - selects a residue named X
resid X - selects a residue with the number X
not hydrogen - do not display hydrogen atoms
Examples:
resid 1 to 7
resid 8 9 10
C7800 Introduction to molecular modelling - exercise -20Exercise
4
1. How many atoms does the model contain?
2. How many units contains cucurbit[n]uril?
3. What happens to water molecules at the interface of the simulation box?
4. What functional groups contains the axis?
5. What is the total charge of the axis?
6. Try to visualize the model as it is shown on the page 15.