C7800 Introduction to molecular modelling - exercise -1Section
Modelling
Programs for molecular modelling II
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 -2Exercise
1
1. In a text editor, create a file in the xyz format describing the water model with the
following parameters. The length of OH bonds will be 1 Å. The HOH bond angle will be
90°. Save it to your home directory as "water.xyz".
2. Load the created file into the VMD program.
3. Verify the actual bond length and the size of the HOH angle. (VMD Main > Mouse >
Label, VMD Main > Graphics > Labels)
4. Display the water molecule in the following models: Lines, CPK, Licorice, VDW.
C7800 Introduction to molecular modelling - exercise -3-
OpenBabel
Format conversion by openbabel:
$ module add openbabel
$ babel input.xyz output.mol2
alternatively:
$ babel -ixyz input.txt –omol2 output.out
List supported formats:
$ babel -L formats
http://openbabel.org/wiki/Main_Page
Open Babel is a chemical toolbox designed to speak the many languages ​​of chemical data.
It's an open, collaborative project allowing anyone to search, convert, analyze, or store
data from molecular modeling, chemistry, solid-state materials, biochemistry, or related
areas.
Help:
$ babel -H
capital H
C7800 Introduction to molecular modelling - exercise -4Exercise
2
1. Activate the module openbabel.
2. List the formats that the installed version openbabel supports.
3. Convert the file water.xyz to the format Sybyl Mol2 format and save it as water.mol2.
4. Open the file water.mol2 in a text editor and discuss the meaning of its contents.
5. Convert the file water.xyz to the format InChI and save it as water.txt.
6. Open the file water.txt in a text editor and discuss the meaning of its contents.
C7800 Introduction to molecular modelling - exercise -5Exercise
3
1. Load into the program Avogadro molecule from the file water.xyz.
2. Optimize its geometry. What is the optimal bond length and bond angle?
3. Display the molecule in various graphical representations.
4. Load the file water.xyz into the program Nemesis (Import Structure -> OpenBabel)
5. Display the molecule in various graphical representations.
6. Optimize its geometry. What is the optimal bond length and bond angle? Compare
with results obtained in Avogadro. Explain any differences.
C7800 Introduction to molecular modelling - exercise -6Exercise
4
1. In Sketch Structure project in the program Nemesis, draw the structure of benzoic acid.
2. Convert the molecule to a 3D representation (Structure > Convert to 3D). Rate the
quality of the conversion.
3. Repeat the same procedure for cyclohexane.
C7800 Introduction to molecular modelling - exercise -7Exercise
5
1. Build C60 in Avogadro using SMILES.
2. Find "Buckminsterfullerene" topic in Wikipedia and get SMILES representation of the
molecule.
3. Build the model (Build > Insert > SMILES …).
4. Optimize and polish the model if necessary.