Conformational Comparison Opcodes

The commands in this section are used to describe criteria for considering conformations to be distinct. These commands are used in the contexts of conformational search and minimization of multiple conformations.

The opcodes in this section are linked below:

MSYM — use the MmSYM library

ADDC — ADD Conformation

MULT — MULTiconformer minimization

CHIG — CHIrality checking (Global)

COMP — structure atom COMParison

CRMS — Convergence RMS

ATEQ — ATom EQuivalencies

NSEQ — Numbering System EQuivalencies

NSRO — Numbering System ROtation

NSRF — Numbering System ReFlection

NANT — do not consider eNANTiomers to be duplicates

DEMX — Delta-E MaX energy windowing

NORE — NO REordering done on output structures

MSYM — use the MmSYM library

mmsym is a library that is used to identify a good map of atoms between two conformers for use in comparing these conformers. If the conformers are not dramatically different, this map will be the best one possible.

If mmsym is used, ATEQ, NSEQ, NSRO, and NSRF are unnecessary and are ignored. Comparisons can be done in place (molecules will not be translated or rotated while finding the map). If conformations are not being done in place, the structures written to the output structure file are positioned to minimize the RMS difference in the atomic positions of the comparison atoms between the first structure written and all subsequent structures.

Note: MSYM requires at least three atoms to be specified for comparison using the COMP operation code. The COMP opcode may appear before or after the MSYM operation code.

mmsym is the recommended mechanism for eliminating redundant conformers.

Relevant DEBG flag: 82

ADDC — ADD Conformation

ADDC is used to eliminate redundant conformers from a collection of conformers. Each time ADDC is executed it tries to add the current structure to the collection of conformers. The same checks for redundancy and transformations, such as net translation and rotation of the current structure, are performed as in a multiple minimization of conformers (see COMP) but no minimization or energy estimation is conducted. Energies from earlier MacroModel or Jaguar calculations may be used as part of the comparison process (see DEMX). If MacroModel energies are to be used then a FFLD line with the same force field as used to calculate the energies must precede the ADDC line.

MULT — MULTiconformer minimization

Perform multiconformer minimization, i.e., delete duplicate structures as defined by the COMP command after minimization of each structure. If neither MULT nor COMP is used, then no elimination of duplicate structures is done and every energy minimized structure appears in the output file. If COMP is used without MULT, then multiconformer minimization is performed and the maximum number of structures saved is limited to 10000.

This command is appropriate only for a file of different conformations of the same molecule as would be produced by a previous conformational search. It most often is used with MINI to “polish” the results of a previous conformational search, using more stringent convergence criteria than were used in the search itself.

Note: MULT must appear before MINI in the .com file.

CHIG — CHIrality checking (Global)

This command identifies and saves the chirality of the atoms listed in the arguments, and rejects structures whose chirality has changed during the calculation. The chirality is stored only for the first structure in the input file. All structures are subsequently checked against the chirality of the first. Used with MULT, MCSM, MCMM, LMCS, LMC2, and LOOP for files of identical structures differing only in conformation.

Use as many CHIG commands as necessary to save all important chiralities.

CHIG commands must come after the READ command in the .com file. With MCMM searching, chirality is checked after the Monte Carlo step and also after the following energy minimization.

COMP — structure atom COMParison

Arg1-4 are atom numbers to be used for comparing a minimized structure with all previous unique minima found. COMP may be specified up to 50 times to allow up to 200 atoms to be used in the comparisons. If COMP is not specified, the program will not attempt to eliminate duplicate minima. Structures are considered the same unless the least squares superimposition of the compared atoms finds one or more pairs of equivalent atoms separated by more than the separation given by the CRMS command (default = 0.25 Å). It is not necessary to specify all atoms in a molecule for comparison, but a representative sampling from widely separated points in the structure should be given in COMP commands.

CRMS — Convergence RMS

Sets the geometric criterion which defines two structures to be identical within a conformational search or a multiple minimization. Despite the command name, the program uses as its criterion not the root-mean-square interatomic distance after optimal rigid-body superposition of a pair of structures, but rather the maximum distance between corresponding atoms after superposition. You can override this default and select the RMSD instead.

ATEQ — ATom EQuivalencies

This command is used with COMP commands to allow the identification of nonunique structures having symmetrical atoms (e.g., the two oxygens of a carboxylate ion or the ortho/meta pairs of carbons of a phenyl ring). We suggest using MSYM rather than specifying atom equivalences using ATEQ. If such equivalent atoms are present (and listed as comparison atoms in COMP commands), then identical conformers having different atom numbering systems will emerge as different, unique final structures. To avoid this duplication, ATEQ commands are used to note equivalent atoms. A different ATEQ command is used for each equivalent atom set and may equivalence up to 4 atoms in each set.

ATEQ commands normally only cyclically permute the atoms listed for comparisons of conformations. However, search techniques such as LMOD (LMCS) and LLMOD (LMC2) can result in non-cyclic permutations. Specifying DEBG 79 causes non-cyclic permutations to also be considered in comparisons of conformations.

For example, if a molecule has four carboxylates and a trimethyl ammonium, then one would include five ATEQ commands, 4 for the carboxylates (2 equivalent atoms) and 1 for the trimethyl ammonium (3 equivalent atoms) if all atoms were included in COMP commands. Alternatively, such symmetrical atoms may be left out of the comparison lists. For high symmetry cases, it is better to replace ATEQ with NSEQ, NSRO, and NSRF commands. In such cases a better alternative would be to use MSYM.

In applying the ATEQ commands, the program will generate all permutations of equivalenced atoms to try for a near perfect geometrical match (i.e., find a duplicate conformer). Such an approach will generate, inter alia, some nonsense permutations with clustered equivalent atoms (e.g., phenyl rings) but such permutations will never match and do not cause problems.

Turning on DEBG 81 causes full information to be printed.

NSEQ — Numbering System EQuivalencies

We suggest using MSYM rather than specifying atom equivalences using NSEQ.

This command allows the user to list alternative numbering systems for the molecule. For each alternative numbering system, you will need as many NSEQ commands as you have COMP commands. The COMP command can be considered as the original numbering system of the comparison atoms. Each block of NSEQ commands corresponds an alternative numbering system for the comparison atoms listed in the COMP command. For united atom butane for example, the COMP command might contain arg1-4 as 1 2 3 4, then the NSEQ command would contain as the only possible alternative numbering system 4 3 2 1. An alternative to this simple case would be to use NSRF. See the MacroModel User Manual — Contents for more complex examples.

NSRO — Numbering System ROtation

We suggest using MSYM rather than specifying atom equivalences using NSRO.

This is intended primarily for use on symmetrical cyclics. This feature will cause the program to compare not only corresponding atoms, but also all possible rotations of the numbering system. Used with completely symmetrical systems such as cycloalkanes with the comparison command, arg1 should be 1. Used with systems like 18-crown-6, arg1 should be 3 (note that this will not eliminate all duplicates with 18-crown-6—to do this, use the NSEQ commands). NSRO automatically turns on the NSRF option so that enantiomeric conformations are eliminated (this feature can be disabled with the NANT command). All atoms in the ring being rotated must be listed in the COMP commands. Furthermore the atoms listed in COMP commands must be in the order in which they occur in the ring. Atoms not in the ring (hydrogens or other substituents) should not be listed.

NSRO must come before READ or TRED commands and after COMP commands.

NSRF — Numbering System ReFlection

We suggest using MSYM rather than specifying atom equivalences using NSRF.

If invoked, this feature will cause the program to compare not only corresponding atoms but also numbering system reflections. Used with symmetrical structures such as normal acyclic alkanes with the comparison command. This command reverses the ordering of the atoms in the COMP commands for comparison purposes, thus atoms in the COMP commands must be given in the order of the atoms in the chain.

NSRF must come before READ or TRED commands.

NANT — do not consider eNANTiomers to be duplicates

Ordinarily, enantiomers are considered identical for the purpose of conformational comparisons. This command, which alters this behavior, takes no arguments.

DEMX — Delta-E MaX energy windowing

DEMX sets a window for permissible energy above the lowest-energy conformation. This command discards any structure that is more than arg5 kJ/mol above the minimum energy conformation. Since more than one force field may be used in a command procedure, arg1 is a code that is matched to a corresponding “energy code” in a MINI command. DEMX is used with MULT and MCMM commands. If no DEMX is used, then all energy minima will be kept regardless of their relative energies. We use this command to limit the energy range of the conformers printed out at the end of the procedure. We suggest a value of 25.0 kJ/mol (ca. 6 kcal/mol) for arg5 to prevent output of high-energy structures. If you plan to do a subsequent solvation treatment, a 50.0 kJ/mol window may be more appropriate to allow for major reordering of structures on inclusion of solvation. However, it is better to include solvation (SOLV command) directly in the minimization.

A second energy window may be set in arg6 (suggested value 1.5-2 times that in arg5), which is used to reject structures before complete minimization by a check of the relative energy at iteration number arg2. Aborting the minimization of structures whose energies appear too large part way through the minimization makes the overall procedure faster.

NORE — NO REordering done on output structures

Normally, MULT and conformational search output structures are reordered in increasing energy. If this command is specified, this reordering is suppressed.

NORE must come before READ or TRED commands.