MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatFor some torsional arrays, it may be desirable to add higher order parameters. This may bedone for V 4 -V 6 terms by adding an additional line of torsional parameters and beginning theline with a 54 as shown below:4 C3 - C3 - C3 - H1 0.0000 0.0000 0.2670 0000 00Si 0000 000054 0.1000 0.0000 0.5000The parameters above specify V 3 = 0.267, V 4 = 0.100, and V 6 = 0.500.Parameters in the file must be ordered from most specific to most general since the programwill assign the parameters to interactions the first time a valid match is found between themolecule and the parameter line. Thus in the example of the two torsional interactions above,the more specific one given first must come first in the force field file. That will allow theprogram to apply the correct v3 term (0.350) if there are two hydrogens (H1) on atom 2—otherwiseC3-C3-C3-H1 interactions will use V 3 =0.267.The above paragraphs describe how to specify up to two atoms alpha to (one covalent bondremoved from) each atom in the interaction. By adding up to three additional lines of optionalatom descriptors, up to three beta atoms (connected to an on-interaction atom via two bonds)may be specified for each alpha atom. Consider the three O-H stretching entries below:1 O3 - H2 1.0100 5.0000 -1.0000 1C200 0000 Entry 1O200 00001 O3 - H2 1.0100 5.0000 -1.0000 C200 0000 Entry 21 O3 - H2 1.0100 5.0000 -1.0000 0000 0000 Entry 3The third entry shown here could be the O-H stretch of a simple saturated alcohol. The secondcould specify the O-H stretch of, say, a phenol, which has a C2 (an sp2 carbon) connected to theoxygen. The first entry would not match a phenol, since it specifies that the C2 alpha to theoxygen must be bonded to an O2 (sp2 oxygen). This would match a carboxylic acid.The lines specifying beta atoms have continuation characters immediately preceding the firstset of alpha interactions. In the first entry above, the 1 in the string 1C200 tells the program toread a single line of beta atoms next. This character should be replaced by a 2 or a 3 if there aretwo or three lines of beta atoms. Beta optional atoms appear directly beneath the alpha optionalatom to which they are attached. An alpha atom of type 00 may not have beta atoms specified;however, wild-card types for specific atomic numbers, such as C0, may have beta atoms.Within each group of alpha and beta atoms, more specific combinations must be specified first.For example, if it is desired to match interaction atom X, attached to -A-B and also attached toanother A, the -A-B combination must be given before (to the left) of the unqualified -A attachment.When adding new parameters or modifying old ones, it is wise to use a test structure to be surethe new parameters are being found. If they are not, then you may be using an incorrect atomor bond type or a match is occurring from an entry higher up in the force field file for thestretch, bend or torsional parts of the force field. You may easily test for ordering by puttingMacroModel 9.7 Reference Manual 199