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#1 2018-08-16 03:22:30

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 143
Website

Generate electrostatic potential grid cube based on atomic charges

Today a CCL user asked a question:

Apologies if this is a naive question but I haven't had much success after finding solution
over internet. I want to generate electrostatic potential grid cube file using point charge
model for small molecules. Any suggestion for is highly appreciated. Thank you in advance.

Considering my reply may be useful for some Multiwfn users, I copy my reply here:

You can use Multiwfn (http://sobereva.com/multiwfn) to easily generate electrostatic potential cube file based on atomic charge.

Below is an example of generating such cube file for water:

Write a plain text file named "water.chg" with below content
O       -1.68940800    0.00002500    0.00194100  -0.728713
H       -1.08142400   -0.01012400   -0.78063300   0.364427
H       -1.06246900    0.00994900    0.76945700   0.364286
The 2,3,4 columns correspond to XYZ coordinates in Angstrom, and the last column corresponds to atomic charges.

Then boot up Multiwfn and input
water.chg
5  // Generate grid data
8  // ESP based on atomic charges
2  // Medium quality grid
Then you can use option -1 to visualize isosurface of the grid data, or use option 2 to export the grid data to .cub file.

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#2 2018-10-03 13:16:19

Saran
Member
Registered: 2018-06-07
Posts: 4

Re: Generate electrostatic potential grid cube based on atomic charges

dear sir,

I tried to calculate the electrostatic potential surfaces of molecule by using multiwfn. package. but i could not succeed. the color is not changed which you have mentioned in the manual. here i have attached the image please check
fafa.png


i used the following manual. but i could not succeed.
Plotting electrostatic potential colored molecular surface map
with ESP surface extrema via Multiwfn and VMD

Last edited by Saran (2018-10-03 13:19:03)

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#3 2018-10-03 15:32:20

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 143
Website

Re: Generate electrostatic potential grid cube based on atomic charges

Saran wrote:

dear sir,

I tried to calculate the electrostatic potential surfaces of molecule by using multiwfn. package. but i could not succeed. the color is not changed which you have mentioned in the manual. here i have attached the image please check
https://i.postimg.cc/YjWrnHsF/fafa.png


i used the following manual. but i could not succeed.
Plotting electrostatic potential colored molecular surface map
with ESP surface extrema via Multiwfn and VMD

The most probable reason is that the color scale was not set properly, or coloring method was not properly chosen in VMD.
I strongly suggest you first reproduce the example given in my document to ensure that all your steps are correct.

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#4 2018-10-05 13:24:01

Ihor
Member
Registered: 2018-10-05
Posts: 3

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Sir,

I am a bit confused with units.
I tried 5 – 8 – 6 and successfully obtained ESP.
In output file we have 4 columns. First three (x,y,z) are in angstroms, but ESP is in atomic units.
Is this correct?

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#5 2018-10-05 14:56:22

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 143
Website

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Ihor,

I don't understand what does the 5-8-6 means.
The unit of exported data is always shown on screen, please carefully check the prompts, you will immediately know the unit used.

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#6 2018-10-05 21:16:48

Ihor
Member
Registered: 2018-10-05
Posts: 3

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Tian Lu,

Thanks for Your rapid response.
Unfortunately, I still can't find unit of exported ESP.

5 - 8 - 6 means followed sequence:
5  // Generate grid data
8  // ESP based on atomic charges
6  // Input center coordinate, number of points and extension distance

Then I input all grid data and generate ESP file.
However, as You may find in the attached picture (last line) unit of potential is still unknown.
Since all grid coordinates in the exported file are in angs., I am not sure, that ESP is exported in a.u.
image.png

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#7 2018-10-06 08:46:17

sobereva
Tian Lu (Multiwfn developer)
From: Beijing
Registered: 2017-09-11
Posts: 143
Website

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Ihor,

The unit of the calculated function is a.u.

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#8 2018-10-06 09:11:04

Ihor
Member
Registered: 2018-10-05
Posts: 3

Re: Generate electrostatic potential grid cube based on atomic charges

Many thanks for the response

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