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Are there any dedicated Python tools/packages/scripts that help me convert a SMILES structure into an MD coordinate and topology file (both for GROMACS and just the single one for LAMMPS)?

Demonstrate this task with two example SMILES:

1. 'C1CC[13CH2]CC1C1CCCCC1'
2. '[*]CC(c1ccccc1)[*]'
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  • $\begingroup$ Have you looked into github.com/Isra3l/ligpargen ? It builds OPLS -AA parameters from the smiles. $\endgroup$ Commented Jan 25 at 6:42
  • $\begingroup$ Does it have to be python? Can you open it in avogadro and then save as an xyz file? $\endgroup$ Commented Jan 30 at 2:49
  • $\begingroup$ @RoshanShrestha what if I want to build CHARMM parameters? $\endgroup$
    – Pranoy Ray
    Commented Feb 23 at 21:40
  • $\begingroup$ @VladislavGladkikh what do you mean? please elucidate your comment $\endgroup$
    – Pranoy Ray
    Commented Feb 23 at 21:42
  • $\begingroup$ @PranoyRay For charmm, you need to look into its database since it's not automated like the ligpargen server. $\endgroup$ Commented Feb 25 at 15:35

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Obtaining 3D structures from SMILES is reasonably easy. There are many tools, some of which are written in Python, that allow you to do this. RDKit comes to mind, you can see this answer for an example.

Automatically creating reliable topologies, on the other hand, is hard. I'm not aware of any tools that would universally, and reliably, create a topology from a SMILES string to any force field you wanted. There are force field specific tools, as Roshan pointed out in the comments. Some of them you can run on your own machine (like LigParGen), some are only hosted on a webserver.

Here are some examples, although I'm sure there are other tools available:

  1. LigParGen - OPLS - https://traken.chem.yale.edu/ligpargen/
  2. SwissParam - CHARMM - http://swissparam.ch/
  3. ATB - GROMOS - https://atb.uq.edu.au/
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