Topology

ORAC is instructed to read the topology file by the command

READ_TPG_ASCII field.tpg

of the &PARAMETERS environment. File field.tpg contains information on the series of residues needed to define the topology of the actual solute molecules. This information is provided through a series of free format keywords and their corresponding input data as done in the main input file sys.mddata. In this way, ORAC  reads the solute connectivity, the atomic charges, the atomic labels corresponding to those found in the PDB file, and the atomic types according to the chosen force field (i.e. AMBER, CHARMM or others). Moreover, the atomic groups and the improper torsions are also defined.

As for the mail input file, the file field.tpg is parsed and the composing substrings of each line are interpreted. Comment lines must have the ``#'' character in column 1. Each residue or unit definition starts with the keyword

RESIDUE residue_name

where residue_name is a character label which must match labels found in the command JOIN of the environment &PARAMETERS, and must end with the keyword RESIDUE_END. These residue delimiting keywords are the only one in capital letters in field.tpg (see the valine example later on in this section)

Atom type definitions and charges are read in between the keywords atom and end. For each atom three strings must be entered: the PDB atom label, the potential type according to the selected force field as specified in parameter file (see Sec.10.3.1) and the point charge in electron units. Groups are composed of all atoms entered between two successive group keywords. The PDB labels must be all different from each others since they are used to establish the topology and connectivity of the solute.

The bond connectivity is specified between the keywords bond and end by providing the series of bonds present in the residue. Each bond is specified by two atom labels corresponding to the atoms participating to the bond.

All possible bendings and proper torsions are computed by ORAC from bond connectivity and need not to be specified. Improper torsions must instead be provided. Improper torsion are used to impose geometrical constraints to specific quadruplets of atoms in the solute. In modern all-atoms force fields, improper torsions are generally used to ensure the planarity of an $sp_{2}$ hybridized atom. The convention in ORAC to compute the proper or improper torsion dihedral angle is the following: If ${\bf r}_{1}, {\bf r}_{2}, {\bf r}_{3}, {\bf r}_{4}$ are the position vectors of the four atoms identifying the torsion, the dihedral angle $\chi$ is defined as

$$\chi = arcos \left [{({\bf r}_{2} - {\bf r}_{1} ) \times ({\bf r}... ...{\bf r}_{3} - {\bf r}_{2} \vert \vert{\bf r}_{4} - {\bf r}_{3} \vert } \right ]$$ (10.2)