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.
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).