Visualizing Vibrational Modes Generated by MacroModel

Vibrational modes from MacroModel calculations can be visualized in Maestro using The ePlayer or the Low Mode Vibrational Sampling Panel. Two opcodes, VIBR and VBR2, generate structures for a set of selected vibrational modes. VIBR is used for small molecules, whereas VBR2 is used for larger molecules of the order of seven residues or larger. VBR2 utilizes the same techniques as a large-scale low-mode conformation search, which include using ARPACK routines to solve the large eigenvalue problem. The arguments to VIBR and VBR2 specify the first and last mode to visualize, as well as the number of frames to include for the period of each vibration. Rotational and translational modes are automatically disregarded. The structural output consists of a series of frames (structures) that together animate the vibration when imported and played in Maestro’s ePlayer.

VIBR and VBR2 computations are started from the command line with an appropriate command file and an input structure file. The input structure should be minimized to a low gradient. Below is a sample command file for a VIBR calculation.

vibr.mae
vibr-out.mae
 FFLD      10      1      0      1     1.0000     0.0000     0.0000     0.0000
 SOLV       3      1      0      0     0.0000     0.0000     0.0000     0.0000
 EXNB       0      0      0      0     0.0000     0.0000     0.0000     0.0000
 BDCO       0      0      0      0    89.4427 99999.0000     0.0000     0.0000
 READ       0      0      0      0     0.0000     0.0000     0.0000     0.0000
 CONV       2      0      0      0     0.0200     0.0000     0.0000     0.0000
 MINI       1      0    500      0     0.0000     0.0000     0.0000     0.0000
 VIBR       1      5      5      0     3.0000     0.0000     0.0000     0.0000

The command file specifies vibr.mae as the input structure file, and the output structural animations will reside in the file vibr-out.mae. The following four opcodes specify the potential settings, here MMFFs as the force field with solvation, extended non-bonded cutoffs, and BDCO usage for electrostatic interactions. After the structure is read, a minimization is requested (CONV, MINI). The VIBR opcode selects the first five non-trivial modes for animation, with five frames per quarter vibration cycle.