Re: [Rdkit-discuss] Autodock Vina
Hi Valik, I do this on a regular basis for our generators here. Basically what you will need is to: 1. Generate 3D structures for the molecules (RDKit can do that) 2. Save to SDF files (again, RDKit) 3. Convert to PDBQT (I use OpenBabel: "$ obabel -isdf structures.sdf -opdbqt -Oname-.pdbqt -m") Then you'll have the files you need. Of course, you will still need to build the pdbqt file for the target and the vina_config file, but that you only need to do once. All the best, -- Gustavo Seabra. On Tue, Jun 22, 2021 at 4:08 AM Velik Velikov wrote: > Dear all, > > > > I am constructing new molecules (de novo design) that are drug-like with > RDKit. I have my molecules in SMILES now and I need to check them with > AutoDock Vina. I have never used it and I have been trying since last week > but I kind of don’t know where to go from here. > > What is my config file, ligand or receptor? Do I need MGL Tools, PyMOL or > something else? > > Also, I couldn’t run it on my mac - Big Sur, I tried with a VirtualBox but > it didn’t work out either. I am thinking about installing Autodock Vina on > my old windows laptop now. Appreciate any help with this tool. Thanks in > advance. > > > Best, > > Velik Velikov > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Autodock Vina
Hi Velik, This is a discussion list for the RDKit, not for Autodock Vina. Here's the link for getting help about Autodock Vina: http://vina.scripps.edu/questions.html Best, -greg On Tue, Jun 22, 2021 at 10:08 AM Velik Velikov wrote: > Dear all, > > > > I am constructing new molecules (de novo design) that are drug-like with > RDKit. I have my molecules in SMILES now and I need to check them with > AutoDock Vina. I have never used it and I have been trying since last week > but I kind of don’t know where to go from here. > > What is my config file, ligand or receptor? Do I need MGL Tools, PyMOL or > something else? > > Also, I couldn’t run it on my mac - Big Sur, I tried with a VirtualBox but > it didn’t work out either. I am thinking about installing Autodock Vina on > my old windows laptop now. Appreciate any help with this tool. Thanks in > advance. > > > Best, > > Velik Velikov > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] autodock vina pdbqt file to mol2
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 -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] autodock vina pdbqt file to mol2
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 -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] autodock vina pdbqt file to mol2
Jan,
On Fri, May 9, 2014 at 9:17 PM, Jan Domanski jan...@gmail.com wrote:
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...
The mol2 parser assumes that all Hs are present, so it sets a flag on every
atom saying that it has no implicit Hs.
You can manually undo this:
In [23]: m =
Chem.MolFromMol2File('Downloads/conformer_132_out_1.mol2',sanitize=False)
In [24]: for atom in m.GetAtoms(): atom.SetNoImplicit(False)
In [25]: m.UpdatePropertyCache()
In [26]: mh = Chem.AddHs(m,addCoords=True)
In [27]: print mh.GetNumAtoms()
69
I skipped sanitization entirely when I read the molecule in. This is to
prevent the assignment of radicals.
Note that the mol2 parser is really only even remotely tested with output
from Corina; if you end up with alternate atom types, you should anticipate
further problems.
-greg
--
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Re: [Rdkit-discuss] autodock vina pdbqt file to mol2
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 -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Is your legacy SCM system holding you back? Join Perforce May 7 to find out: #149; 3 signs your SCM is hindering your productivity #149; Requirements for releasing software faster #149; Expert tips and advice for migrating your SCM now http://p.sf.net/sfu/perforce___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
