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The Calculation Window
The calculation window sets the calculation type and conditions, selects the molecule, and specifies the output. Click Select Molecule 1..., Load Molecule, select 1caa.pqr from the folder you saved it to, then OK. All of the files created in the APBS run will be stored in the Project folder; unique project folders within the current working directory are automatically used if no others are specified. By default, the electrostatic potential and solvent accessible surface files will be created in OpenDX format in the project folder. This can be changed by clicking on Output files but these will be sufficient for our purposes as will the parameters in the Mathematics section. Note that you can save the Grid, Physics and Mathematics settings for future calculations or load settings from previous calculations. |
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The Grid Window
The grid window allows the user to specify the grid dimensions, resolution, and center while visualizing the grid. Click on Show Coarse/Fine Grid then Autocenter and Autosize. If you have the psize script in your path you can click on Psize Auto Params to generate the recommended grid parameters. Be sure that the coarse grid always extends significantly beyond the molecule in all dimensions and that the coarse grid is at least 1 Å larger than the fine grid. Since Rubredoxin is so small you will need to adjust one of your grids after using Psize Auto Params. Also be sure that the machine you are working on has enough memory to work with the grid you are interested in. For the best performance, you should have a bit more physical memory free than the Memory to be allocated indicated at the bottom of the Grid tab (otherwise your operating system will use your hard disk as extra memory, slowing down the calculation). |
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The Physics Window
The physics window allows the user to set additional physical parameters and to add ions to their calculation. It is important to note that quantitative results (e.g., solvation and binding energies) will depend sensitively on the protein dielectric, and the surface definition. The commonly used solvent probe radius is 1.4 Å for solvent and 0.0 Å for vacuum calculations. The solution is by default ion-free. To add ions, click Add, and then specify the properties of your ion. Make sure your solution is neutral. We have finished setting up the calculation. |
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3. APBS execution
Return to the Calculation tab. You can save an APBS profile by clicking Save Profile. To run the calculation click Write APBS Parameter file, Run APBS, (or just click Run APBS--this will automatically write the APBS Parameter file). Open a shell (in Windows, click Start, Run, then type in cmd.exe and click Ok) and paste the line of text that appears after clicking Run APBS. It can be helpful to pipe the output to a file for future inspection. The execution will be automated in future versions.