Usually Valve is run by:
To check if Valve is installed and works properly try to issue following commands:
valve.py --help valve.py --version
We will use 1ns 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 lets have a look at the protein of interest. Start PyMOL and get
1cqz PDB structure (for example by typing in PyMOL command prompt
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¶
Lets load another structure. Open file
1cqz_sample_topology.pdb (see Test data). It is a first frame of the MD simulation and it is en example of how the frame of MD looks like. In order to create Object definition you have to discover following things:
- What is the name of water molecules?
- What are numbers of residues in the active site?
- What size the active site is of?
It is also a good idea to open
.pdb file in your favorite text editor and look at residue numbers and names.
Prepare config file¶
Valve performs calculations according to the configuration (aka config) file.
Things to remember:
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.
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.
Improve clusterization of Inlets. See Configuration file options for more hints on available clusterization options.
Give us your opinion. Send your questions, inquires, anything to developer(s): firstname.lastname@example.org. This are couple of questions that might be useful to form your opinion.
- What do you like in Valve and Aqua-Duct?
- What do you do not like in Valve or Aqua-Duct?
- What is missing?
- Do you find it useful?