AIM analysis from PDB electron density maps

mverissi · 2022-02-19 01:29:20

Dear all,

I am interested in comparing AIM results from wave function / DFT calculations with those performed directly on electron density maps from PDB structures. Is it possible to do it using MultiWFN? I suppose MultiWFN cannot read PDB files and calculate the corresponding electron density maps, so does anyone know of a code that could read the maps and save the electron density in a format that MultiWFN could read?

Best regards,

Marcos Verissimo Alves
Physics Department, ICEx
Universidade Federal Fluminense
Volta Redonda, Brazil

sobereva · 2022-02-19 04:54:02

Dear Marcos Verissimo Alves,

Multiwfn is able to load pdb file and calculate promolecular density (superposition of density of atoms in their isolated states). However, this density is quite crude, if you need relatively realistic density you should perform quantum chemistry calculation based on the geometry to obtain wavefunction file.

Multiwfn also supports loading experimental density if it is recorded in .cub/.vti/.dx/.grd format, but topology analysis is not formally supported in this case.

Best regards,

Tian

mverissi · 2022-02-19 05:08:53

Dear Prof. Lu,

Thanks for the reply. I have indeed been performing exploratory DFT and xTB calculations for active sites of proteins with MultiWFN over the last few months, and now I’m about to start DLPNO-CCSD(T) calculations with ORCA, aiming to perform AIM analysis with them. It’s a pity that MultiWFN doesn’t support AIM analysis for experimental charge densities. Is there a fundamental limitation, or is it just not implemented for reasons, say, of priorities?

Would you know of any code that would perform AIM analysis on experimental charge densities? It would be fundamental for the project I intend to undertake with those calculations. I would still use MultiWFN for the theoretical calculations, since it’s a great code and I found it quite easy to work with.

Best,

Marcos

sobereva · 2022-02-19 06:43:58

Dear Marcos,

I think it is not important to perform AIM analysis based on experimental density. As long as the calculation level is good enough (e.g. PBE0 with def2-TZVPP), the quality of electron density is already satisfactory. Due to limited resolution, the experimental density is not necessarily better than theoretical density.

According to my experience, GFN-xTB density is too poor for AIM analysis. ORCA is unable to generate density at DLPNO-CCSD(T) level.

Although Multiwfn doesn't formally support AIM topology analysis based on experimental density, due to the very flexible design of Multiwfn, it is still possible to perform AIM topology analysis based on electron density grid data, please check this post for example: http://sobereva.com/wfnbbs/viewtopic.php?pid=2276. However, please bear in mind, this feature was not sufficiently tested since it is rarely used.

Best regards,

Tian

mverissi · 2022-02-19 15:10:48

Hi Tian,

Once again, thanks for the reply. My intent is to see if AIM and/or NCI analysis, applied to experimental electronic densities, would give any information about the protonation states of charged residues such as histidine in active sites.

It's good to know that Multiwfn does AIM on grid-based densities. I guess I'll give it a try and see what happens.

Best,

Marcos

Multiwfn forum

#1 2022-02-19 01:29:20

AIM analysis from PDB electron density maps

#2 2022-02-19 04:54:02

Re: AIM analysis from PDB electron density maps

#3 2022-02-19 05:08:53

Re: AIM analysis from PDB electron density maps

#4 2022-02-19 06:43:58

Re: AIM analysis from PDB electron density maps

#5 2022-02-19 15:10:48

Re: AIM analysis from PDB electron density maps

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