MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatWithin the Main Parameter Section of the force-field, lines beginning with I>0 have thefollowing meanings:1. Constants for stretching interactions2. Constants for bending interactions3. Constants stretch-bend interactions4. Constants for dihedral interactions5. Constants for improper torsional (or OPB) interactions6. Van der Waals constants for pairs of atoms7. Constants for hydrogen bonding interactionsToward the right in these lines optional atom descriptors may be given. These list additionalatom types which must be attached to each of the main atoms at the left of the parameter linefor a valid match. Each descriptor consists of a 4-character field (e.g., 0000 or C200) specifiestwo attached optional atoms. 00 is the wild card atom type symbol. Thus 0000 specifies thatthere are no required attachments to the corresponding main atom (i.e., just match the mainatoms and bonds). C200 says that a C2 (an sp2 carbon) must be bound to the main atom inquestion. A C2C3 indicates that both a C2 (sp2 carbon) and a C3 (sp3 carbon) must be bound.Optional atom fields of each force field file entry must not be left blank in the force field file. Ifno special attachments to any main atoms are required, then use a 0000 for each atom in theinteraction. For stretches there 2 optional atom fields (corresponding to the two main atoms ofthe stretch interaction). For a bend, there are 3 optional atom fields, for a torsion, there are 4such fields. Consider the torsional entry from a force field file below as an example:v1 v2 v34 C3 - C3 - C3 - H1 0.0000 0.0000 0.3500 0000 H1H1 0000 0000^ ^ ^ ^ ^ ^ ^ ^atm1 atm2 atm3 atm4 Optional atoms for atom: 1 2 3 4The entry above specifies that anytime a C3 - C3 - C3 - H1 torsional array is found in whichtwo hydrogens (H1’s) are attached to main atom 2, then the torsional force constants given (V 1= 0.0, V 2 = 0.0, and V 3 = 0.35) will be used. Now consider the following torsion force fieldentry:4 C3 - C3 - C3 - H1 0.0000 0.0000 0.2670 0000 0000 0000 0000^ ^ ^ ^ ^ ^ ^ ^atm1 atm2 atm3 atm4 Optional atoms for atom: 1 2 3 4The entry above notes that when any C3 - C3 - C3 - H1 array is found, then the forceconstant V 3 =0.267 will be used regardless of the substitution of any atom (including atom 2).This is because all optional atom entries are 0000. Both of the above lines may appear in aforce field because matching is done top down: the first time an acceptable match is found, theparameters from the matching force field line will be used.198MacroModel 9.7 Reference Manual