Talk:Poisson–Boltzmann profile for an ion channel

General announcements
This resource was used as part of the lecture and practical session on electrostatics calculations for the Wellcome Trust and Systems Biology Doctoral Training Centre postgraduate course on computational biochemistry, University of Oxford (Michaelmas 2007). The lecture is on WebLearn at http://tinyurl.com/282dfd (restricted access; a similar lecture without access restriction is in the resource near the top).

Feel free to go to lunch as soon as you have entered your result! I hope you all had fun. Please fill in the feedback form!

There will be no debrief session after lunch. But as the results come in to the table below, think about the possible sources of error and the general shape of the profile. See virtual debrief session below. To get in touch with me by email, look me up at University of Oxford contact search. – Kaihsu 12:40, 5 December 2007 (UTC)

APBS issues
APBS is installed in /usr/apps/apbs-0.5.1-ia32/bin/apbs. You can make an alias for it in the bash shell: alias apbs=/usr/apps/apbs-0.5.1-ia32/bin/apbs Then just type apbs, followed by the parameters, to use it. Or, you can add it to your path (the environment variable PATH ).

Use this input file: nAChR.in. Do not copy the input file from the PDF file: it is truncated!

PDB2PQR settings
Use all the default settings on the PDB2PQR server: do not change anything! This ensures that your colleagues' results are comparable. In case PDB2PQR does not work, get this one from WebLearn: 1OED.pqr.

Results
You might want to report your results here, in addition to plotting it with your colleagues:



Virtual debrief session
If someone is keen, they can post a plot of the results (using gnuplot, xmgrace , or any other plotting software) as they come in.

What are the possible sources of error in this profile? How do we estimate the error? Has anybody tried to (carefully and knowledgeably) change the grid-point numbers?

What are the implications of this profile? (To start, which side is extracellular and which cytoplasmic? 30 &Aring; or 120 &Aring;?) Think the distinction between thermodynamics and kinetics.

We have a set of scripts in our lab to automate the pore-scanning process in parallel on a compute cluster. Get in touch if you would like to take a look (and possibly improve it!).

– Kaihsu 12:40, 5 December 2007 (UTC)

Code for automation
I wrote some Python code to automate this process. The job submission requires a queuing system called Grid Engine. Copyright &copy; 2008 Kaihsu Tai. Moral rights asserted (why?). Hereby licensed under either GFDL or GNU General Public License at your option.

Obviously, you will have to change the parameters in the driver-functions ( main ) to fit the purposes of this tutorial. That is the exercise for the reader! – Kaihsu 16:12, 23 December 2008 (UTC)

Also, you will need to generate the PQR file, along with a file containing a list of the coordinates for the sample points. The script submits the job to a queueing system called Grid Engine, but you can submit the job by hand if you do not have this installed. – Kaihsu 11:04, 9 January 2009 (UTC)

Additionally, you will need to change the ion species. – Kaihsu 17:03, 30 January 2009 (UTC)

See also Two-dimensional Poisson–Boltzmann profile for an ion channel. – Kaihsu 13:07, 30 April 2009 (UTC)