Q samples (not yet udated for the Q5-package)

Note: To run the simulations in the examples, you need to set up a directory with some files common to all the examples, as described below.

1. Linear interaction energy method for absolute binding free energy calculations

For more information on the linear interaction energy (LIE) method, please see

• Hansson et. al., J. Comput.-Aided Mol. Des., 12, 27-35, (1998)

1.1. Binding free energy of the glucose/galactose binding protein complex with glucose

Get all the files, as a tar file (for UNIX) or as a zip file (for MS Windows) to work with the example.
For the background and theory of this example please see

• Åqvist and Mowbray, J. Biol. Chem.., 270, 9978-9981

In this example, we will calculate the affinity of the glucose/galactose binding protein for glucose by sampling a glucose molecule's interactions with water and in the binding site of the solvated protein.

1.2  Binding free energy of the fatty acid binding protein complex with stearate

Get all the files, as a tar file (for UNIX) or as a zip file (for MS Windows) to work with the example.

In this example, we will calculate the affinity of the fatty acid binding protein for stearate by sampling a stearate molecule's interactions with water and in the binding site of the solvated protein.

2. Free energy perturbation calculation of relative binding free energy

2.1. Relative binding free energy of methotrexate and an analogue for DHFR

Get all the files, as a tar file (for UNIX) to work with the example.
For the background and theory of this example please see

• Graffner Nordberg et al., J. Med. Chem. 2000, in press

In this example, we will calculate the relative free energy of binding of methotrexate and the methotrexate analogue N-[4-[(2,4-diaminoquinazoline-6-yl)methoxycarbonyl]benzoyl] L-glutamic acid by free energy perturbation simulations.

This sample is in a very crude state - no description is available yet, only the set of input files. The most important part of this example is the complicated FEP file, which makes use of most of Q's features for redefining interaction parameters.

 Setting up the samples directory

1. Download the compressed archive with files common to all the samples:
   • Tar file (for UNIX)
   • Zip file (for MS Windows)
2. Decompress the file:
   • on a UNIX system, use a command like:

     tar -xvf qsamples_common.tar

   • on Windows, use your favourite zip software.

   This step will create a directory called qsamples.

3. Set up the Q programs

   A. Using the evaluation kit:

   Extract the files from the evaluation kit archive file in the qsamples directory created in step 2.

   Add the qsamples directory to your search path.

   B. Using the licensed programs:

   Make sure the directory where the Q executables are is in your search path.