MacroModel Reference Manual - ISP

Appendix D: Force-Field File Formatboth the united atom and the all atom force field parameter sets. Thus, for the all atom chargeset, the charges given are for the heavy atoms plus any attached hydrogens. To get the actualcomplete all atom charge set, the program uses dipoles from the main section of the field(mainly for heteroatom-H’s) or from the substructure (mainly for C-H’s).By using a combination of bond dipoles and formally united atom charges, MacroModel reproducesboth AMBER field charges exactly and also provides reasonable charges for substitutedor modified residues. As such, it allows the use either charge set (from the All atom or Unitedatom paper) and, independently, hydrogens on carbons or united atoms. As we supply the field,the charges correspond to those given in the older AMBER paper (i.e., the united atom paper),but you may switch to charges from the newer paper (i.e., the all- atom paper) by modifyingthe ALT 1 line at the top of the force field file.You will notice that many of the parameters for some of the more complex amino acidsidechains (phenol, indole, imidazole, etc.) are given separately from the actual residue itself inthe substructure section of the force field file. This allows any such substructure to be given thesame parameter set as used in the actual amino acids. Thus indole itself gets the same parameterset as the indole of tryptophan. Such substructures are labeled as “C” (for Continue, seebelow) which means that the atoms matching the substructure may also be matched againstsubstructures further down in the force field (i.e., where the actual residue might be found).The residues themselves are labeled “S” (for Stop). This means that once atoms are matched(as a complete residue), then they are removed from candidacy for matching with substructureswhich come below them in the field. This distinction speeds substructure matching since eachsuch match of a “S” substructure removes atoms which must be tested from subsequentmatching.Amber Torsional SpecificationThere are three differences between the MacroModel and the AMBER torsional parameters.These differences do not affect the actual functional forms used by the program, but only theway in which parameters are specified.First, AMBER uses a different entry for each 2-fold (n=2) and each 3-fold (n=3) barrier;MacroModel uses a single entry with both 2-fold (V 2 ) and 3-fold (V 3 ) barriers included.Second, AMBER uses only positive torsional potentials but uses an angular offset (γ) to adjustthe position of minima and maxima. For γ=0˚ or γ=180˚, this is best accomplished in Macro-Model through the use of positive and negative Vn values, as follows.AMBER n=3, γ= 0˚: use V 3 /2 directlyAMBER n=3, γ=180˚: use –V 3 /2 for V 3 /2AMBER n=2, γ= 0: use –V 2 /2 for V 2 /2208MacroModel 9.7 Reference Manual