Setup

Setting up a simulation model

It will normally be necessary to follow steps 1 to 6 of the PDB Files tutorial when setting up a simulation model for a protein from a PDB file. However, in this case, the proteins are very simple — consisting of only standard amino acid residues — and perusal of the structures indicates that there are no non-hydrogen atoms with undefined coordinates. This means that the much simpler approach of Example 19 in the pDynamo distribution suffices to generate molecular mechanics models of the proteins.

Example program: Setup.py

Each of the PDB files contains several structural models, as is often the case with protein structures determined via NMR spectroscopy. By default, the PDBFile_ToSystem method will take the structure of the first model from the file. To explicitly specify that the nth model be chosen, employ the argument modelNumber = n (noting that n starts at one).