Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins
The following implementation of the above equation uses the programming language Python together with the Molecular Modeling Toolkit (MMTK) by Hinsen [1]. To run the program, you need Python, MMTK, ScientificPython, and Numpy installed on your computer. The program was tested using Python-2.2, MMTK-2.2, ScientificPython-2.4.1, and Numpy-21.3.
To run the program type "./s2predict.py pdbfile s2file outfile" or "python2 s2predict.py pdbfile s2file outfile". It takes a PDB file and a S2-order parameter file as input and writes the result to outfile. If S2-order parameters are not available, one can create (e.g. by hand) a dummy file with non-zero S2 values with the same format as the file ubq.s2.dummy . For PDB files that contain proton coordinates, it is useful to remove all protons first and have them subsequently added in standard positions by the program using MMTK. Note: For multiple chain proteins (for example HIV protease described in the paper), the program needs to be modified (create additional chains and loop over them to add their heavy atoms to the atom list).
