Input to ORAC : Force Field and Topology Files

Compared to molecular liquids, simulating any complex macromolecule, poses additional problems due to the covalent structure of the systems and to the related complexity of the potential force fields. ORAC  builds the covalent topology needed to evaluate the potential energy from the structure of its constituents. In case of a protein the constituents are the amino acids. Also, ORAC tries to to minimize the size and the complexity of the actual input needed to construct this topology.

In practice, the minimal information to be provided in order to describe the residue topology is the constituent atoms, the covalent bonds and, in case of polymers or biopolymers, the terminal atoms used to connect the unit to the rest of the chain. In addition, in order to assign the correct potential parameters to the bonds, bending and torsions of the residue, the type of each atom needs to be specified. Finally, to each atom type must correspond a set of non-bonded parameters.

When the bonding topology of the different residues contained in the solute molecule(s) is known, the units are linked together according to their occurrence in the sequence. In this fashion the total bonding topology is obtained. From this information, all possible bond angles are collected by searching for all possible couples of bonds which share one atom. Similarly, by selecting all couples of bonds linked among each other by a distinct bond, torsions can be obtained.

The following sections describe the format of the topology and force field parameters files read by ORAC . The reading of the two files is carried out immediately after the command READ_TPF_ASCII and READ_PRM_ASCII in the environment &PARAMETERS are encountered in the input file. The topology and force field parameters files are strongly dependent from each other and together fully define the molecular force field of the solute molecule(s). In the ORAC distribution archive the most recent AMBER[4] force field and topology files are provided.