I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows:

 (1) Adding hydrogens: AllChem.AddHs
 (2) Compute 3D coordinates: AllChem.EmbedMolecule
 (3) Clean-up with force field: AllChem.MMFFOptimizeMolecule

--But I would like to take into account different solvents so that the 3D structure more closely resembles in vitro activity. For example, an in vitro screen where small molecules are diluted in (1) DMSO or (2) ethanol or (3) water.

--I know that Psi4 can estimate properties in different solvents. But I have been unable to find a python library that generates an actual 3D structure that's optimized for solvents (e.g. a solvent-specific force field that would be applied after the 3D coordinates have been computed as in the RDKit example above).

--Any help/suggestions on how to do this (preferably using python) would be much appreciated.

  • 1
    $\begingroup$ Probably better suited for Matter Modelling SE: mattermodeling.stackexchange.com $\endgroup$ – S R Maiti Mar 20 at 17:49
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    $\begingroup$ Psi4 is an electronic structure code, not a force field code. You can use your force-field geometry in Psi4 as a starting point and further optimize it including a solvent model. The other option is to stick with force-field methods and add explicit solvent molecules to your system. Take a look at Gromacs. $\endgroup$ – Feodoran Mar 20 at 18:35

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