Solvate and Equilibrate Target Protein¶
Quick floe search term: CPD A1
In this tutorial, we will show you how to use the SPRUCE-prepared beta-lactamase protein in an MD preparation floe Solvate and Equilibrate Target Protein.
Tip
This floe should take approximately one hour to run and cost ~$3.
Search and Run the Floe in Orion¶
Locate the floe in Orion¶
Start by using the left hand vertical navigation tabs on your Orion home page to go to Floe page.
On the Floe page, click on the Floes tab, where you will find the list of the available floes and packages.
Click on a small caret next to Packages (under Filter Floes By section on the left) to expand the list of packages and click on the OpenEye Cryptic Pocket Detection Floes package. This will ensure that the floes listed in the middle of the page are from the Cryptic Pocket Detection package.
From this list, click on the Solvate and Equilibrate Target Protein Floe, and then click on the blue LAUNCH FLOE button in the bottom right corner of the page to launch the Job Submission Form.
Provide Input Files and Parameters to Run the Floe¶
- Output path:
Select the destination for your output data by specifying the Output path.
- Input Data:
Choose the Target Protein to be the SPRUCE prepared dataset for beta-lactamase.
- Output Data:
You can customize the output dataset and collection names under the Output Data options.
- Force Field:
You can change the force fields for protein and ligand by selecting from options available for Protein Parameters and Ligand Parameters.
- Solvent Options:
By default, this floe solvates target protein in water-xenon mixed-solvent with 150 mM xenon and 150 mM NaCl salt. By changing Solvent Molar Fractions and Solvents input parameters, you can change the concentration of xenon probes for a mixed-solvent simulation or set up a single-solvent simulation by changing the Molar fractions to 1.000, Solvents to tip3p, and Salt Concentration to 150 mM.
Caution
If you change Solvent Molar Fractions and Solvents parameters to run single-solvent simulation, you will be able to perform only exposon analysis for cryptic pocket detection. Probe-occupancy or dynamic probe-binding analysis for cryptic pocket detection cannot be performed on the data generated by a single-solvent simulation.
Job Submission Form¶
Click on the green Start Job button a the bottom right corner of the page.
If the job completed successfully, there should be an MD dataset, a reference PDB file containing all of the system components, an h5.tar.gz file, and a collection generated.