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
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