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")
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
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
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
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
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 =
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
7 matches
Mail list logo
