User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30

(Difference between revisions)

Revision as of 12:32, 5 February 2013

Project name

From the assigned computer, a new terminal was created from either of the following steps:

1. Finder > Services > New terminal at folder

-or-

2. press the provided shortcut key F5

Then enter $maestro to open the suite.
Draw the molecule on the workspace area. Modifications can be made through the Edit panel > build > fragments > atom properties. Sponge the drawn molecule for clarity.
To save the molecule, create this entry on the project table -or- from the workspace option > project entry > name and create the project and then save.
The next step is to put the molecule under energy minimization to find a stable energetically conformation.

To initiate energy minimization, go to the Applications option > Impact > Minimization.
Minimization analyzes the molecule using Classical Physics.
A dialog box appears with the force field set on OPLS 2005.
Then click the Minimization tab. On the maximum cycles, this was changed to 10,000. The other standard parameters such as gradient criterion (0.01) and energy change criterion (1e-07) were kept. The pH was changed to the desired pH level of 7.4.
Knowing there are amino acids present, by changing the pH of the parameters, the structure must also be converted to its alkoxide form at pH 7.4. As a result, through atom types O3 was changed to OM.
After all the parameters were set for minimization, the host zorro was chosen and the minimization was started.

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 * To save the molecule, create this entry on the project table -or- from the workspace option > project entry > name and create the project and then save.
 * The next step is to put the molecule under energy minimization to find a stable energetically conformation.
+* To initiate energy minimization, go to the Applications option > Impact > Minimization.
+* Minimization analyzes the molecule using Classical Physics.
+* A dialog box appears with the force field set on OPLS 2005.
+* Then click the Minimization tab. On the maximum cycles, this was changed to 10,000. The other standard parameters such as gradient criterion (0.01) and energy change criterion (1e-07) were kept. The pH was changed to the desired pH level of 7.4.
+* Knowing there are amino acids present, by changing the pH of the parameters, the structure must also be converted to its alkoxide form at pH 7.4. As a result, through atom types O3 was changed to OM.
+* After all the parameters were set for minimization, the host zorro was chosen and the minimization was started.