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

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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.
* 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.
* 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.




Revision as of 09:32, 5 February 2013

Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

Molecular Fingerprinting and Docking of Compounds to the ADA active site

  • 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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