Protein Constant pH Simulations Panel

Run MD simulations on a protein over a range of pH values with the continuous constant pH MD method, to determine pKa values for titratable residues.

To open this panel: click the Tasks button and browse to FEP+ → Constant pH Simulations.

  • Overview
  • Using
  • Features
  • Additional Resources

Overview of Protein Constant pH Simulations

The simulations are performed with the continuous constant pH method [13], referred to as CpHMD. The method uses an extended Hamiltonian to simultaneously propagate spatial (real) and titration (virtual) coordinates. Simulations are performed at steps in the pH value (much like lambda steps in FEP), and replica exchange is performed periodically for replicas with adjacent pH values. The result is a set of titration curves for each titratable residue in the protein; from these curves the pKa value of the residue is extracted.

Using the Protein Constant pH Simulations Panel

This panel allows you to generate pKa values for the titratable residues in a protein (currently restricted to ASP, GLU, HIS, LYS, and CYS). You can choose individual residues, which are listed in the panel, or you can choose one or more of these residue types to generate pKa values for all residues of the selected types.

The output from the simulation is a text file named jobname_pka.txt and zipped tar archive named jobname_11-out.tgz. The text file is set up in columns, containing

  • the site number starting from1
  • the residue name as chain:residue
  • an inequality sign < or > if the pKa value is out of the pH range
  • the pKa value
  • the Hill coefficient

The tar archive contains plots in PNG format of the titration curve (S, the fraction of the deprotonated state, as a function of pH). The plot files are named jobname_siteN_titr.png where N is the site number as listed in the text file.

Constant pH simulations are run in the μVT ensemble by default, which uses GCMC sampling of water molecules. It has a variable number of water molecules with a fixed chemical potential (μ) and a fixed number of solute atoms (N). See Grand Canonical Monte Carlo Addition of Water for more information.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see constant_ph Command Help.

To generate both macro pKa values and micro pKa values from the results of a constant pH MD simulation, see cphmd_calc_pka.py Command Help.

Protein Constant pH Simulations Panel Features

Load structures from option menu

Choose the structure source for the constant pH simulations.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries. When this option is selected, a Load button is displayed to the right.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries. When this option is selected, a Load button is displayed to the right.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

Load button

Load the structures from the Project Table or Workspace into the panel.

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Select titratable residues for pKa calculation check list

Check the boxes for individual titratable residues that you want to include in the calculations. At least one box must be checked for the calculation to run, whether by checking the boxes directly, or by selecting residue types using the Select link.

Select link

Select all residues in the list that are of a the chosen types. Opens a pane in which you can check the boxes for the residue types and apply the selection to the list. Partially checked boxes indicate that only some (but not all) residues of the given type are selected in the table.

Using pH range text and Change link

Displays the current pH range used for the titration curve and the simulation settings. If the selection is APS/GLU/HIS/CYS, then the recommended range is 0-8. If the selection is LYS, then the recommended range is 7-13. If the selection is ASP/GLU/HIS/CYS and LYS, then the recommended range is 0-13. Uncapped CYS residues are not currently allowed.

Click the Change link to open the Constant pH Advanced Options Dialog Box for making the changes. The pH range should span the expected pKa values, with a margin of 1 – 2 units on either side. Longer simulation times can improve the accuracy of the results, at the expense of longer computation time.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Protein Constant pH Simulations - Job Settings Dialog Box, where you can make settings for running the job.

If you have purchased FEP+ Web Services, the Submit to Web Services option is present. Select to upload the job to FEP+ Web Services for execution, and click the Submit button. The number of credits to be used and the number of available credits are reported, and the job is uploaded on confirmation of the credit usage for the job. If you have access to multiple Web Services projects, you are prompted to choose the project to associate the job with. The FEP+ Web Services Job Table Panel opens.

If you have Web Services credentials but do not see the Submit to Web Services option, see Troubleshooting.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Reset button

Reset the panel to its default settings.

Tutorials

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