Model coordination complex using GROMACS or CP2K

Question

Is it possible to compute a 3D model of a calcium EDTA complex and it's energy? If so, how should I go about doing it or where can I obtain relevant information regarding computation methods?

I searched through the docs of GROMACS and CP2K, but didn't find relevant information.

Answer 1

Here is how you can get the structure from PubChem, read the SMILES into Avogadro2, do a MMFF94 (classical) optimization, and then a single-point energy calculation using NWChem (RHF, 6-31G*). The Avogadro2 Input builder will create a CP2K file if you prefer. For GROMACS, there is extensive documentation that includes at least one example of how to set up a single-point calculation.

Note: there are many choices for doing this procedure, including level of theory, basis sets, tools, and so on. That said, you can follow this flow and do the geometry optimization at a higher level of theory and follow that up with a single-point calculation if you choose.

Everything here works fine on a stardard Ubuntu 22.04 LTS build.

1. Go to the PubChem entry for Calcium disodium EDTA;

2. Scroll down to section 2.1.4 (Canonical SMILES) and copy the string:

C(CNH+CC(=O)[O-])NH+CC(=O)[O-].[Na+].[Na+].[Ca+2]

into a text file and call it something like CaEDTA.smi (use the SMILES format extension);

3. Open Avogadro2 and load the CaEDTA.smi file, you should see something like:

4. Under the Extensions tab, go to Open Babel and Optimize Geometry, which will slightly change the positions of the atoms and give you an optimized geometry using the MMFF94 force field, which is more than adequate for the job;

5. Go to the Input tab and select NWChem; change the Filename Base to CaEDTA (or something more descriptive); change Calculation Type to Single Point; and change Theory to RHF; and save this file as CaEDTA_MMFF94-opt_HF-631star_energy.nw;

6. If you have not installed NWChem, do sudo apt install nwchem;

7. On the command line run the following:

nwchem CaEDTA_MMFF94-opt_HF-631star_energy.nw >& CaEDTA_HF-6-31star_energy.out &;

8. After about 7 minutes, the job will finish. At that point, do the following:

grep -B2 -A5 "Total SCF energy" CaEDTA_MMFF94-opt_HF-631star_energy.out

which will print to screen:

9. Note that if you ingest the .out file into Avogadro2, you will see a wacky structure. This is not unexpected, nor is this "correct." However, the steps are here. You might consider adding water molecules and/or using the COSMO (or related) solvent models; and

10. Information about the all the above can be found (at least) in the NWChem documents.