Valve tutorial

This tutorial assumes aquaduct and Valve is already installed - see Aqua-Duct installation guide. It is also assumed that user is acquainted with Valve manual and Valve Configuration file options.

Valve invocation

Usually Valve is run by:

valve.py

To check if Valve is installed and works properly try to issue following commands:

valve.py --help
valve.py --version

Test data

Mouse!

We will use 1 ns MD simulation data of sEH protein (PDBID 1cqz). This simulation was performed in Amber 14. Necessary files can be found at Aqua-Duct home page in section download. Required data is in the sample data file.

Inspect your system

Before we start any calculations let’s have a look at the protein of interest. Start PyMOL and get 1cqz PDB structure (for example by typing in PyMOL command prompt fetch 1cqz).

To setup Valve calculations we need to know the active site of the protein. More precisely we need to know IDs of residues that are in the active site. This would allow us to create Object definition.

But wait. Is it really the correct structure? How many chains there are? What is the numeration of residues? How does it compare with the topology file from sample data?

Create Object definition

Leti’s load another structure. Open file 1cqz_sample_topology.pdb (see Test data). It is a first frame of the MD simulation and it is an example of how the frame of MD looks like. In order to create Object definition you have to discover following things:

  1. What is the name of water molecules?
  2. What are numbers of residues in the active site?
  3. What size the active site is of?

Note

It is also a good idea to open .pdb file in your favorite text editor and look at residue numbers and names.

Create Scope definition

Scope definition is easy to create. We will use Convex hull version so the scope definition could be simply backbone.

Prepare config file

Valve performs calculations according to the configuration (aka config) file.

Lets start from dumping config file template to config.txt file. Open it in your favorite editor and fill all options. If you have troubles look at Configuration file options (and Valve manual).

Things to remember:

  1. Provide correct paths to topology and trajectory data.
  2. Enter correct Object and Scope definitions.
  3. Make sure visualization is switched on.

Run Valve

Make sure all necessary data is in place. Open terminal, go to your working directory and type in:

valve.py -c config.txt

Depending on your machine and current load it may take a while (matter of minutes) to complete all calculations.

Visual inspection

In the last stage PyMOL should pop up and Valve should start to feed it with visualization data. This would take a moment and if you set up save option a PyMOL session would be saved. Once it is done Valve quits and switches off PyMOL. Now, you can restart it and read saved session.

Clusterization

Improve clusterization of Inlets. See Configuration file options for more hints on available clusterization options.

Analysis tables

Open 5_analysis_results.txt file and look at summaries and tables. See also Valve manual.

Feedback

Give us your opinion. Send your questions, inquires, anything to developer(s): info@aquaduct.pl. There are couple of questions that might be useful to form your opinion.

  1. What do you like in Valve and Aqua-Duct?
  2. What do you do not like in Valve or Aqua-Duct?
  3. What is missing?
  4. Do you find it useful?