Re: [Rdkit-discuss] autodock vina pdbqt file to mol2

[TJ O'D. <tj...@ac...>]

Babel can read and write both pdbqt and mol2 files. I'm not sure how the
atom ordering might be accomplished though.

TJ
On May 9, 2014 2:43 PM, "Jan Domanski" <ja...@gm...> wrote:

> Thanks for the quick reply Christos!
>
> I found the pdbqt_to_pdb script that you mentioned but a google search for
> a pdbqt to mol2 yield nothing (other than this thread). the pdbqt_to_pdb
> converter is very crude: it retains only the best pose from _out.pdbqt and
> it basically just strips the BRANCH and ROOT tags deposited by autodock
> (which I was doing anyway with the sed).
>
> The main problems remaining are atom order (I can fix that) and missing
> hydrogens (can't fix that). There is a mode where I can prevent the
> prepare_ligand4.py from removing the hydrogens – but the output poses then
> have really weird geometry.
>
> But let's refocus a little bit: this is not an autodock vina question
> (although many folks here are knowledgeable enough to help me). This is a
> question on a mol2 file to which it should be possible to add Hs with rdkit
> and it's somehow not happening (at least not in my hands). My mol2 could be
> somehow malformatted.
>
>
>
>
>
> On 9 May 2014 20:57, Christos Kannas <chr...@gm...> wrote:
>
>> 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
>>
>> Researcher
>> Ph.D Student
>>
>> Mob (UK): +44 (0) 7447700937
>> Mob (Cyprus): +357 99530608
>>
>> [image: View Christos Kannas's profile on LinkedIn]<http://cy.linkedin.com/in/christoskannas>
>>
>>
>> On 9 May 2014 20:17, Jan Domanski <ja...@gm...> 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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>>
>
>
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