Hi Jan,
AutoDock has a set of tools (MGLTools) that have tools to convert pdb to
pdbqt and vice-versa.
If I recall it can also convert pdbqt to mol2 also. See this discussion
http://autodock.1369657.n2.nabble.com/ADL-pdbqt-to-mol2-td6755769.html
Best,
Christos
Christos Kannas
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On 9 May 2014 20:17, Jan Domanski <jan...@gmail.com> wrote:
> Hi guys,
>
> I'm really stuck here: I have some output from autodock vina in a rather
> obscure pdbqt format. It's a little bit like pdb but not quite. I'm trying
> to get back a mol2 file.
>
> The autodock pdbqt file has only the polar hydrogens in it – part of the
> trick is to re-add the hydrogens.
>
> Example autodock vina output is attached (it's a conformer of the ACE
> native ligand DUDE).
>
> First of all, I convert that to a PDB file by doing a simple sed,
> sed -e '/ROOT/d' -e '/BRANCH/d'
> Then I reorder the atoms to match those of the original
> crystal_ligand.mol2 (because autodock re-orders the atoms duh).
>
> Finally, I save a mol2 file out (attached) ordered as the original
> crystal_ligand and with polar hydrogens (for each pose of a conformer).
>
> Let's go to rdkit and try to add hydrogens:
>
> mol = Chem.MolFromMol2File(output, removeHs=False)
> mol2 = AllChem.AddHs(mol, addCoords=True)
> print mol.GetNumAtoms(), mol2.GetNumAtoms()
> 44 44
>
> So, only the implicit hydorgens are present. Calling AddHs doesn't raise
> an error and it doesn't really change the number of hydrogens...
>
> Now this may not be the best way of doing things: what I care for is to
> get a mol2 from autodock vina that I can compare to the original mol2 from
> DUD (same atom order, same number of atoms). Maybe there are other ways to
> achieve this: one idea would be to inject the docked pose coordinates into
> the original mol2 atoms (heavy and polar hydrogens) and somehow "adjust"
> the non-polar hydrogens.
>
> Thanks,
>
> - Jan
>
>
>
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