ADL: AutoDockFR: how to prepare ligands for covalent docking?

Gao Zhenting zhentgpicasa at gmail.com
Sun Oct 11 17:11:51 PDT 2020


Dear Sanner,

Thanks for the help. Following your suggestion, I can generate ligand pdbqt
file for covalent docking with AutoDockFR now.
To do a successful covalent docking, the matching atom definition of both
receptor and ligand is very critical.
It would be nice if more details are added to the covalent docking tutorial.

Best regards
Zhenting

Michel Sanner <sanner at scripps.edu> 于2020年10月11日周日 上午1:12写道:

> Hello
>
>
>
> *From: *Gao Zhenting <zhentgpicasa at gmail.com>
> *Date: *Saturday, October 10, 2020 at 7:02 AM
> *To: *Michel Sanner <sanner at scripps.edu>, "autodock at scripps.edu" <
> autodock at scripps.edu>
> *Subject: *AutoDockFR: how to prepare ligands for covalent docking?
>
>
>
> Dear Sanner,
>
>
>
> I am learning covalent docking workflow of AutoDockFR. And I finished the
> the tutorial.
>
> The ligand is provided for the tutorial, but there seems no document about
> how to prepare the ligand.
>
>
>
> I noticed that 4 atoms from sidechain of cysteine is included in the
> ligand pdbqt file, and they are put at the head of the pdbqt file, with
> atom index ranging from 1~4. If I regenerate the ligand file by
> prepare_ligand4.py, then the 4 atoms will be move at the end of the pdbqt
> file with index ranging from 23~26. With the regenerated ligand pdbqt file,
> the covalent docking pose is wrong, with a positive docking score.
>
>
>
> Yes, this is correct. The ROOT / ENDROOT block of atoms has to contain the
> atoms forming the covalent bond and be the root of the torsion tree because
> these atoms should not move as the conformation of the ligand is modified
> during docking.’
>
> If you run prepare_ligand4.py you need to specify which atom to use as a
> root for the torsion tree. If nothing is specified, prepare_ligand4.py will
> pick a central atom. The root atom can be specified using -R on the
> prepare_ligand4.py command line. I recommend running prepare_ligand4.py a
> first time on the ligand, then look at the file and find the number of the
> atom you want to be the root and re-run prepare_ligand4.py with -R Num to
> change the torsion tree and make sure the atoms forming the covalent bond
> are at the root.
>
>
>
> With the files you sent me, running
>
>
>
> prepare_ligand4.py -l
> 3c9w_ligandWithSideChain_random_prepared_covalent_out.pdbqt -o
> ligandWithCorrectRoot.pdbqt -R 25
>
>
>
> should create a ligand with the correct atoms in the root
>
>
>
>
>
> -Michel
>
>
>
> Could you help me on how to prepare the ligand file?
>
>
>
> Best regards
>
> Zhenting
>
>
>
> Commands of my workflow:
>
>
>
> ~/tools/MGLTools-1.5.6/bin/python
> /home/zhentg/tools/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py
> -l ../../data/3c9w_ligandWithSideChain_random.pdbqt -o
> 3c9w_ligandWithSideChain_random_prepared.pdbqt
>
> ~/tools/ADFRsuite-1.0/bin/adfr -l
> 3c9w_ligandWithSideChain_random_prepared.pdbqt -t 3c9w_cov_cmdline.trg
> --jobName covalent -C 1 2 3 --nbRuns 8 --maxEvals 100000 -O --seed 1
>
> ~/tools/ADFRsuite-1.0/bin/adfr -l
> 3c9w_ligandWithSideChain_random_prepared.pdbqt -t 3c9w_cov_cmdline.trg
> --jobName covalent -C 26 25 24 --nbRuns 8 --maxEvals 100000 -O --seed 1
>


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