Electrostatic potential surfaces

[Bruce]

Apologies in advance if this is a case of RTFM.

I have watched the nice instructions at https://www.youtube.com/watch?v=khr4mp7HiuQ. However, when I try perform the same task and create an electrostatic potential surface, Avogadro pops a window that says “Error Electrostatic potential surfaces are not yet supported.” I have tried both Windows and Ubuntu installs of Avogadro.

What am I doing wrong?

Thank you.

[ghutchis]

We changed this up. You can map an electrostatic potential on top of a Van Der Waals surface - which is usually what people want.

In the early beta versions, we allowed mapping the electrostatic potential itself. On some simple molecules, this was fine (e.g., the video). On moderately complex molecules, the surface is extremely complex and is almost impossible to generate an accurate surface.

A full tutorial is in the manual

[ghutchis]

Since this seems to be a common Google search, you can also find more here:

Electrostatic potential

I think what you want is to generate the electrostatic potential mapped onto the molecular surface (i.e, the van der Waals surface). In version 1.x, do this: Set the surface type to Van der Waals Set the “color by” to Electrostatic Potential (this will use Gasteiger charges) Change the resolution if you wish That’s it. You’re right that at the moment, this is not possible in Avogadro 2 (beta). [57 PM]

[Ahmed_Subrati]

How can I use the rainbow color palette for electrostatic potential, instead of the faded red and blue palette? Thanks.

[ghutchis]

At the moment (in Avo 1.2) you can’t. This seems to be a common request, so I’ll make sure both options are in Avo 1.3 to be released by the end of the summer.