Vrms

Vrms provides the symmetry-corrected root-mean-square deviation (RMSD) between a series of test conformations of a drug-like molecule and a reference conformation. Two modes of operation are available.

In the first mode, which is suitable for comparing the conformations of a molecule free in association, the test conformation is rotationally and translationally superposed on the reference conformation before the RMSD is computed.

In the second mode, which is designed for comparing docked conformations of a ligand with the crystal structure, no superposition is performed, since all conformations are specified relative to the protein target.

Vrms can correct for global and local symmetries. For example, if the test conformation differs from the reference conformation by a 180º rotation of a benzene ring, the local symmetry of the benzene is detected and applied so that a low RMSD is obtained.

User Options

Command-line options provide detailed user control, including:

use of symmetry
use superposition
information to be logged in the output file, such as which symmetry relations were applied in a given comparison.

Windows User-Interface

The MS Windows version of Vconf includes a convenient graphical user interface that facilitates assigning parameters, running Vrms, and viewing its results. The interface brings together Vrms, our molecular display program Vdisplay, and helpful Vrms support utilities, as shown in the following screen-shots. (Click
images for full-sized views.)

Vrms version 1.0 for MS Window2000/XP including a graphical user interface and Linux..

References

Identification of symmetries in molecules and complexes. Chen, W., Huang, J., & Gilson, M.K.; J. Chem. Inf. Comput. Sci., 2004, 44, 1301-1313.

Calculation of partial charges and resonance forms: Fast assignment of accurate partial atomic charges. An electronegativity equalization method that accounts for alternate resonance forms. Gilson,M.K., Gilson,H.S.R. & Potter,M.J.; J. Chem. Inf. Comput. Sci. 2003, 43(6), 1982-1997.