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.

[John]

Hello, has Avo 1.3 been released with this option? I want to create electrostatic potential graphs using the full rainbow colour palette, but this still doesn’t seem to be an option…

[Farid_Rafie]

Hello,

I used Avogadro to generate an electrostatic potential map for my molecule, and I would like to include it in my paper. However, I am unsure about the basis of this calculation in Avogadro. I apologize if my question was unclear before.

As an example, in another paper, the authors mentioned the following for the electrostatic potential map (EPM) part:
Electrostatic Potential (MEP) map can be utilized. All geometries were optimized through density functional theory (DFT) with the B3LYP functional and the Stoddard basis set, specifically the sum +6-31G(d) basis. These calculations were conducted using the Gaussian 03 program package.

Thank you for your help.

[ghutchis]

I’m not sure I understand your question. Do you want to know how to write that you generated electrostatic potential maps using Avogadro for a research manuscript?

[Farid_Rafie]

Thank you for your response.
Yes, I want to know that how Avogadro generates Electrostatic potential maps? For example in that research paper authors mentioned DFT with a specific basis set? What should I mention about the setting that I use for my EPM when I use Avogadro?

[ghutchis]

Apologies for the delay. You’d want to say something like:

Electrostatic potential surface depicted using Avogadro version X [citation] mapping atomic Gasteiger charges on the molecular van der Waals surface.

In general, Avogadro 1.0 / 1.2 uses Gasteiger charges from Open Babel. I don’t usually see discussion of particular options as far as depictions / graphics.

[Farid_Rafie]

Thank you so much for your response. appreciate it.