Ghemical-GMS/GTK-GAMESS tutorial

Calculating energy difference between axial and equatorial methylcyclohexane at the AM1 level of theory

By Jan H. Jensen

Department of Chemistry

University of Iowa

It is a good idea to read sections 2.1.1-4 in the Ghemical manual before you start.

Screenshots for this tutorial can be found at the bottom of the page.

1. Build and minimize cyclohexane

1.1, Start a new molecular mechanics project

1.2. Build the ring

1.3. Add hydrogens

1.4. Minimize the structure

1.5. Save as “cyclohexane.gpr”

2. Build equatorial methylcyclohexane

2.1. Change an equatorial hydrogen to carbon (select “draw” and click on atom)

2.2. Add hydrogens

2.3. Minimize

2.4. Save as “eqcyclohexane.gpr”

3. Optimize the geometry at the AM1 level of theory using GAMESS

3.1. Go the “Gamess input” menu

3.2. Select “equilibrium geometry” and “AM1”

3.3. Select “review” and add the following line (note the blank space in front the $ sign),


then select “keep”

3.4a. Select submit (this assumes you have installed GTK-GAMESS)

3.5a. Save the file as eqcyclohexAM1.inp (hit OK)

3.6a. Select “start”

3.4b. Select save (if you have not installed GTK-GAMESS

(3.5b. Optional: transfer your input file to another computer)

3.6b. Run GAMESS using a line command

4. Repeat for axial methylcyclohexane

4.1. Select “notebook mode” from Windows menu

4.2. Open cyclohexane.gpr (File menu)

4.3. Repeat Step 2 for axial methylcyclohexane

4.4. Go the “Gamess input” menu

4.5. Select “Review” then “Discard” (This clears the memory of the previous run)

4.6. Repeat steps 3.2. – 3.6. for axial methycyclohexane

5. Calculate the relative energy

5.1. Open eqcyclohexAM1.log in a text editor. Search for this line


5.2. Find this energy a bit above that line (the value of NSERCH will vary and the energy may be different in the last few decimal places).

NSERCH= 24 ENERGY= -40.0805582

5.3. Repeat for axcylcohexAM1.log to find

NSERCH= 26 ENERGY= -40.0782972

5.4. Subtract the energy of the equatorial conformer from that of the axial, and multiply the results by 627.51 kcal mol-1/hartree. You should obtain 1.4 kcal/mol with the equatorial form being lower, which is in good agreement with the experimental free energy difference of 1.7 kcal/mol at room temperature.

You may want to consider using “back-end” programs such as MacMolPlt or third-party programs such as MOLDEN to analyze the log files.

See also: List of suggested GAMESS keywords for large molecules.

Select Screen-shots:

1. Build and minimize cyclohexane

2. Build equatorial methylcyclohexane

3. Optimize the geometry at the AM1 level of theory using GAMESS

4. Repeat for axial methylcyclohexane