ILS Tools Plugin, Version 1.3

This is a graphical user interface for setting up Implicit Ligand Sampling (ILS) calculations using VMD's volmap ils command. For more information about the ILS method please refer to the documentation in the VMD user guide:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node141.html

See also:
Cohen, J., A. Arkhipov, R. Braun and K. Schulten, "Imaging the migration pathways for O₂, CO, NO, and Xe inside myoglobin", Biophysical Journal 91:1844-1857 (2006)

Choosing a probe molecule

You can specify one of the loaded molecules in VMD as the probe in which case you have to set the radius and occupancy manually to the VDW radius and well depth epsilon respectively for each atom. Alternatively you can choose one of the predefined probes from the list.

Choosing a system molecule

Pick the molecular system in which you want to perform the ILS calulation from the list of loaded VMD molecules.

Parameter files

Specify the CHARMM Parameter files you used for the MD simulation.

Aligning frames

At the beginning of the calculation all frames will be align. Specify the atom selection on which the alignment will be based.

Map dimensions

The position and size of the resulting volumetric map.

Other input options

See documentation of the volmap ils command.

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at UIUC
Contact Us // Material on this page is copyrighted; contact Webmaster for more information. // Document last modified on 23 Oct 2009 // 345 accesses since 29 May 2009 .