MacroModel Example: Multi-Structure Conformational Search Using LMOD

An example command file appears below for a conformational search calculation using low-mode conformational searching. Descriptions of the opcodes in the file follow. However, opcodes that are also in the MCMM command file example are not repeated. See the explanations in MacroModel Example: Conformational Search Using MCMM.

serial-lmcs.mae
serial-lmcs-out.mae
 FFLD      10      1      0      1     1.0000     0.0000     0.0000     0.0000
 BDCO       0      0      0      0    41.5692 99999.0000     0.0000     0.0000
 READ       0      0      0      0     0.0000     0.0000     0.0000     0.0000
 LMCS     100      0      0      0     0.0000     0.0000     3.0000     6.0000
 MCSS       2      0      0      0    50.0000     0.0000     0.0000     0.0000
 MCOP       1      0      0      1     0.0000     0.0000     0.0000     0.0000
 DEMX       0    166      0      0    50.0000   100.0000     0.0000     0.0000
 MSYM       0      0      0      0     0.0000     0.0000     0.0000     0.0000
 COMP       0      0      0      0     0.0000     0.0000     0.0000     0.0000
 CONV       2      0      0      0     0.0500     0.0000     0.0000     0.0000
 MINI       1      0    500      0     0.0000     0.0000     0.0000     0.0000

LMCS: Use the Low-Mode Conformational Search method. Arg1=100 means that 100 Monte Carlo steps will be carried out before the calculation stops.

MCSS: Select starting geometries for Monte-Carlo search steps. Arg1=2 tells MacroModel to use as starting geometries structures whose energies are allowed by arg2 and arg5, and are used the fewest times as starting structures.

MCOP: Arg1=1 prints search results every step. Arg4=1 signifies that this is a low-mode serial search. A separate conformational search will be performed on all molecules in the input file. Arg5=0 implies a pure low-mode conformational search, rather than a mixed-mode, as in a previous example.

COMP: Setting arg1=0 allows for all heavy atoms to be compared for each structure in the input file. This removes the need to use atom numbers for the individual structures.