Making molecules with different torsion values automatically

General Discussion
1

Hi there,

I have a molecule, and by going to Analysis > Properties > Torsion Properties, I can change the value of the torsion between four atoms.

I would like to automate this to create a set of molecules, each one from a different torsion number, from the same base molecule.

Any idea how I could script this up?

Ideally I would output X different pdb files for X different torsion values

2

This sounds close to the genetic algorithm to identify multiple conformers of openbabel (link to the documentation with --nconf to set the number of conformers

obabel startingConformer.mol -O ga_conformers.sdf --conformer --nconf 30
       --score rmsd --writeconformers

However I infer your preference of using a GUI is to define which of of the single bonds are free rotors (allowed to rotate). I guess the normal way in Avogadro were to select atom instead (Extensions → calculate → freeze selected atoms) and then launch the algorithm (Extensions → OpenBabel → Conformer Search) and to venture out the options provided there. See here.

3

I would actually suggest doing this with a Python script using Open Babel or RDKit instead. It sounds like you want to match a particular torsion pattern (e.g., with SMARTS) and then write a set of separate angles to separate files.

While I can imagine some ways to do this with Avogadro automation, it’s probably easier to do with a variety of example scripts from RDKit or Open Babel. If you can’t find any, let me know and I’ll post something to GitHub.

1 Like
4

Hey thomas, not really. All I want to do is, for four specified atoms, vary the torsion and have several different versions of the molecule with those different torsion values.

5

Hey there, thanks! I’ve tried open babel but there doesn’t seem to be an obivous way to vary the torsion of a specified set of four atoms, keeping the rest constant like you can do in avogadro. If you know of an easy way it would be much appreciated Prof. Hutchinson!

6

Here’s a version that matches a particular SMARTS pattern: Scan dihedral angles using Open Babel / Pybel · GitHub

If you just wanted to use particular atom numbers (in Open Babel, that’s 1, 2, 3, 4, etc.) you can remove that part of the code with the smarts = pybel.Smarts(…) and change this:

    # get the atom indexes from the SMARTS match
    a = (match[0])
    b = (match[1])
    c = (match[2])
    d = (match[3])

Hopefully it should be commented thoroughly enough to make it clear?

1 Like