Hi all, I was asked to provide figures of the electrostatic potential (mapped to a surface, such as a VdW surface) for several complex small molecules.
GaussView allows one to do that provided some calculations with Gaussian are performed first. With 2 of these molecules, Gaussian seems to go into an infinite calculation loop and after weeks of energy minimization I stopped the calculations.
The Avogadro software is supposed to do that (this is the information provided on the internet, including a detailed manual, i.e. a How To).
When I download and installed avogadro from avogadro.cc then the executable when invoked indicates (in the Surface calculation menu) that the calculation of electrostatic potential surfaces is not yet implemented.
Hence my question: how can I perofm the calculations and provide these pictures ? With proteins it is quite easy using Pymol and the suitable add-on. Apparently not so for much smaller systems (small organic molecules).
Dear Frederic Vellieux,
I don't know how to use Avogadro.cc for doing this but maybe it comes from the version of Avogadro you use... I prefer using version 1.2.0 as it is easier and more functionnal that the ensemble of version 2.0 of Avodagro. Nevertheless, it is very easy to do with VMD (free).
After calculation with gaussian and writing of a *.chk file, I make "formchk ****.chk" to obtain a *.fchk file.
With the utility cubegen:
cubegen 0 density=SCF(or CI) ****.fchk ****-dens.cube
---> to obtain electron density cube file.
cubegen 0 potential=SCF(or CI) ****.fchk ****-pot.cube
---> to obtain electrostatic potential cube file.
After with VMD:
1. In "Main Window" : file > new molecule.
2. In "Molecule File Browser" just opened, "Browse" to find ****-dens.cube.
3. In "Main Window" : Graphics > Representations. In "graphical Representations" opened window you can click on "Drawing Method" and you choose your representation. you can do just whatever you want like "CPK", "Lines" etc... And adjust as you want "sphere scale", "bond radius" etc ...
4. To change colors as you desire : In "Main Window" > "Graphics" > "Colors". In "Colors Controls" opened window you can choose whatever you want. In "Color Scale" bar, you can choose a "Method". For your purpose maybe : "RGB".
5. In "Graphical Representations" window, you can click on "Create Rep": that just clones your representation. Then in "Drawing Method" you choose "Isosurface". You can adjust the "Isovalue" for example 0.001 for having and isosurface of electron density corresponding to Van der Waals surface. You can choose in "Material bar" > "Transparent" or "EdgyGlass" to have a transparent isosurface.
6. In "VMD Main" Window, just right click on the molecule you loaded and then "Load data into molecule". Choose you ****-pot.cube.
7. In "Graphical Representations" just do "Coloring Method" and then "Volume". In the little bar appearing just at right and in front of "Material" bar, choose your ***-pot.cube (by default it will choose ****-dens.cube).
8. Always in "Graphical Representations", you have bars like "Draw style", "Selections", "Trajectory" and "Periodic". Choose "Trajectory"
9. In "Color Scale Data Range" just choose negative and positive value to see appearing you potential electrostatic coloring on the isosurface.
10. When it is okay for you, you can export to an image. Usually I do "File" in "VMD Main" Window and then "render". In the just appeared "File Render Controls" I choose "Tachyon" in "Render the current scene using:" and in the "Render Command" I add just after "%s" the option "-res 1000 1000" you can put the dimensions you want. As well you will have "%s -res 1000 1000 -format TARGA -o ....". And "Start Rendering". You will have your graphical !
As an exemple of VMD I join an image I made.
I hope this could help you !
Hi,
Thanks for your reply.
As I was mentioning there are two molecules for which Gaussian seem to go in infinite calculation loops. So it seems that I cannot use Gaussview for these two molecules. I even tried several computers just in case.
I deinstalled Avogadro and re-installed version 1.2. Read the molecule, performed "optimization" then "Create surfaces". What I obtain when trying ESP is in the enclosed screen capture. I will try to deinstall then try to install Avogadro 2 and see if I can manage then.
Dear Frederic Vellieux ,
If it's not confidential and the molecules are of reasonnable size, I could check the problem by my side in performing the calculations with either Gaussian09 or Gaussian16 on my computer to check if there is a problem if you want.
Well all the small molecules we work on can in principle be patented so that there would be a need to sign an official non-disclosure agreement before I can provide any data... I'll try alternative routes first. But thanks.
I followed the instructions to get WebMO up and running. After setup, when trying to access the admininstration on http://localhost/~fred/cgi-bin/webmo/login.cgi I get the following error message:
Forbidden
You don't have permission to access /~fred/cgi-bin/webmo/login.cgi on this server.
I just used the suggested values during installation instructions, including for setting up Apache.
I am not an expert in web server management but is seems this is a dead end.
Do you know if there is such a service available publically anywhere ?
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