Mod:Hunt Research Group/solvent cavity

visualise in GV6

option1

space filling

• in the Display Format choose Molecule
• change the "Scale Radii by" and push it to maximum, ie 300%
• this is really a form of a spacefilling model
• you can also see the covalent radii by changing the "Atomic Radii" from standard to covalent

option 2

cavity surface

• include "#p sp scrf(smd,solvent=water)" or what-ever your solvent is in the command line
• open the log file in GV
• choose results and "PCM solvation cavity ..."
• switch to show solid and color by atom
• move the slider to make it partially opaque

useful information

• turning on the print option prints some useful information
• such as the surface area and cavity volume.

 GePol: Cavity surface area                          =     81.124 Ang**2
 GePol: Cavity volume                                =     56.942 Ang**3

visualise in JMOL

• to come

visualise in GeomView

• instructions can be found [here]