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
>
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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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