Hi all,
Many thanks for all the responses, Greg's suggestion did the trick!
- Jan
On 10 May 2014 05:32, TJ O'Donnell <t...@acm.org> wrote:
> 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" <jan...@gmail.com> 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 <chriskan...@gmail.com> 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 <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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>>
>>
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